2012生物信息学试卷(英文)
生物信息学英文术语及释义总汇
Abstract Syntax Notation (ASN.l)（NCBI发展的许多程序，如显示蛋白质三维结构的Cn3D 等所使用的内部格式）A language that is used to describe structured data types formally, Within bioinformatits,it has been used by the National Center for Biotechnology Information to encode sequences, maps, taxonomic information, molecular structures, and biographical information in such a way that it can be easily accessed and exchanged by computer software.Accession number（记录号）A unique identifier that is assigned to a single database entry for a DNA or protein sequence.Affine gap penalty（一种设置空位罚分策略）A gap penalty score that is a linear function of gap length, consisting of a gap opening penalty and a gap extension penalty multiplied by the length of the gap. Using this penalty scheme greatly enhances the performance of dynamic programming methods for sequence alignment. See also Gap penalty.Algorithm（算法）A systematic procedure for solving a problem in a finite number of steps, typically involving a repetition of operations. Once specified, an algorithm can be written in a computer language and run as a program.Alignment（联配/比对/联配）Refers to the procedure of comparing two or more sequences by looking for a series of individual characters or character patterns that are in the same order in the sequences. Of the two types of alignment, local and global, a local alignment is generally the most useful. See also Local and Global alignments.Alignment score（联配/比对/联配值）An algorithmically computed score based on the number of matches, substitutions, insertions, and deletions (gaps) within an alignment. Scores for matches and substitutions Are derived from a scoring matrix such as the BLOSUM and PAM matrices for proteins, and aftine gap penalties suitable for the matrix are chosen. Alignment scores are in log odds units, often bit units (log to the base 2). Higher scores denote better alignments. See also Similarity score, Distance in sequence analysis.Alphabet（字母表）The total number of symbols in a sequence-4 for DNA sequences and 20 for protein sequences.Annotation（注释）The prediction of genes in a genome, including the location of protein-encoding genes, the sequence of the encoded proteins, anysignificantmatches to other Proteins of known function, and the location of RNA-encoding genes. Predictions are based on gene models; e.g., hidden Markov models of introns and exons in proteins encoding genes, and models of secondary structure in RNA.Anonymous FTP（匿名FTP）When a FTP service allows anyone to log in, it is said to provide anonymous FTP ser-vice. A user can log in to an anonymous FTP server by typing anonymous as the user name and his E-mail address as a password. Most Web browsers now negotiate anonymous FTP logon without asking the user for a user name and password. See also FTP.ASCIIThe American Standard Code for Information Interchange (ASCII) encodes unaccented letters a-z, A-Z, the numbers O-9, most punctuation marks, space, and a set of control characters such as carriage return and tab. ASCII specifies 128 characters that are mapped to the values O-127. ASCII tiles are commonly called plain text, meaning that they only encode text without extra markup.BAC clone（细菌人工染色体克隆）Bacterial artificial chromosome vector carrying a genomic DNA insert, typically 100–200 kb. Most of the large-insert clones sequenced in the project were BAC clones.Back-propagation（反向传输）When training feed-forward neural networks, a back-propagation algorithm can be used to modify the network weights. After each training input pattern is fed through the network, the network’s output is compared with the desired output and the amount of error is calculated. This error is back-propagated through the network by using an error function to correct the network weights. See also Feed-forward neural network.Baum-Welch algorithm（Baum-Welch算法）An expectation maximization algorithm that is used to train hidden Markov models.Baye’s rule（贝叶斯法则）Forms the basis of conditional probability by calculating the likelihood of an event occurring based on the history of the event and relevant background information. In terms of two parameters A and B, the theorem is stated in an equation: The condition-al probability of A, given B, P(AIB), is equal to the probability of A, P(A), times the conditional probability of B, given A, P(BIA), divided by the probability of B, P(B). P(A) is the historical or prior distribution value of A, P(BIA) is a new prediction for B for a particular value of A, and P(B) is the sum of the newly predicted values for B. P(AIB) is a posterior probability, representing a new prediction for A given the prior knowledge of A and the newly discovered relationships between A and B.Bayesian analysis（贝叶斯分析）A statistical procedure used to estimate parameters of an underlyingdistribution based on an observed distribution. See also Baye’s rule.Biochips（生物芯片）Miniaturized arrays of large numbers of molecular substrates, often oligonucleotides, in a defined pattern. They are also called DNA microarrays and microchips.Bioinformatics （生物信息学）The merger of biotechnology and information technology with the goal of revealing new insights and principles in biology. /The discipline of obtaining information about genomic or protein sequence data. This may involve similarity searches of databases, comparing your unidentified sequence to the sequences in a database, or making predictions about the sequence based on current knowledge of similar sequences. Databases are frequently made publically available through the Internet, or locally at your institution.Bit score （二进制值/ Bit值）The value S' is derived from the raw alignment score S in which the statistical properties of the scoring system used have been taken into account. Because bit scores have been normalized with respect to the scoring system, they can be used to compare alignment scores from different searches.Bit unitsFrom information theory, a bit denotes the amount of information required to distinguish between two equally likely possibilities. The number of bits of information, AJ, required to convey a message that has A4 possibilities is log2 M = N bits.BLAST （基本局部联配搜索工具，一种主要数据库搜索程序）Basic Local Alignment Search Tool. A set of programs, used to perform fast similarity searches. Nucleotide sequences can be compared with nucleotide sequences in a database using BLASTN, for example. Complex statistics are applied to judge the significance of each match. Reported sequences may be homologous to, or related to the query sequence. The BLASTP program is used to search a protein database for a match against a query protein sequence. There are several other flavours of BLAST. BLAST2 is a newer release of BLAST. Allows for insertions or deletions in the sequences being aligned. Gapped alignments may be more biologically significant.Block（蛋白质家族中保守区域的组块）Conserved ungapped patterns approximately 3-60 amino acids in length in a set of related proteins.BLOSUM matrices（模块替换矩阵，一种主要替换矩阵）An alternative to PAM tables, BLOSUM tables were derived using local multiple alignments of more distantly related sequences than were used for the PAM matrix. These are used to assess thesimilarity of sequences when performing alignments.Boltzmann distribution（Boltzmann 分布）Describes the number of molecules that have energies above a certain level, based on the Boltzmann gas constant and the absolute temperature.Boltzmann probability function(Boltzmann 概率函数)See Boltzmann distribution.Bootstrap analysisA method for testing how well a particular data set fits a model. For example, the validity of the branch arrangement in a predicted phylogenetic tree can be tested by resampling columns in a multiple sequence alignment to create many new alignments. The appearance of a particular branch in trees generated from these resampled sequences can then be measured. Alternatively, a sequence may be left out of an analysis to deter-mine how much the sequence influences the results of an analysis.Branch length（分支长度）In sequence analysis, the number of sequence changes along a particular branch of a phylogenetic tree.CDS or cds （编码序列）Coding sequence.Chebyshe, d inequalityThe probability that a random variable exceeds its mean is less than or equal to the square of 1 over the number of standard deviations from the mean.Clone （克隆）Population of identical cells or molecules (e.g. DNA), derived from a single ancestor.Cloning Vector （克隆载体）A molecule that carries a foreign gene into a host, and allows/facilitates the multiplication of that gene in a host. When sequencing a gene that has been cloned using a cloning vector (rather than by PCR), care should be taken not to include the cloning vector sequence when performing similarity searches. Plasmids, cosmids, phagemids, YACs and PACs are example types of cloning vectors.Cluster analysis（聚类分析）A method for grouping together a set of objects that are most similar from a larger group of related objects. The relationships are based on some criterion of similarity or difference. For sequences, a similarity or distance score or a statistical evaluation of those scores is used.CobblerA single sequence that represents the most conserved regions in a multiple sequence alignment. The BLOCKS server uses the cobbler sequence to perform a database similarity search as a way to reach sequences that are more divergent than would be found using the single sequences in the alignment for searches.Coding system (neural networks)Regarding neural networks, a coding system needs to be designed for representing input and output. The level of success found when training the model will be partially dependent on the quality of the coding system chosen.Codon usageAnalysis of the codons used in a particular gene or organism.COG（直系同源簇）Clusters of orthologous groups in a set of groups of related sequences in microorganism and yeast (S. cerevisiae). These groups are found by whole proteome comparisons and include orthologs and paralogs. See also Orthologs and Paralogs.Comparative genomics（比较基因组学）A comparison of gene numbers, gene locations, and biological functions of genes in the genomes of diverse organisms, one objective being to identify groups of genes that play a unique biological role in a particular organism.Complexity (of an algorithm)（算法的复杂性）Describes the number of steps required by the algorithm to solve a problem as a function of the amount of data; for example, the length of sequences to be aligned.Conditional probability（条件概率）The probability of a particular result (or of a particular value of a variable) given one or more events or conditions (or values of other variables).Conservation （保守）Changes at a specific position of an amino acid or (less commonly, DNA) sequence that preserve the physico-chemical properties of the original residue.Consensus（一致序列）A single sequence that represents, at each subsequent position, the variation found within corresponding columns of a multiple sequence alignment.Context-free grammarsA recursive set of production rules for generating patterns of strings. These consist of a set of terminal characters that are used to create strings, a set of nonterminal symbols that correspond to rules and act as placeholders for patterns that can be generated using terminal characters, a set of rules for replacing nonterminal symbols with terminal characters, and a start symbol.Contig （序列重叠群/拼接序列）A set of clones that can be assembled into a linear order. A DNA sequence that overlaps with another contig. The full set of overlapping sequences (contigs) can be put together to obtain the sequence for a long region of DNA that cannot be sequenced in one run in a sequencing assay. Important in genetic mapping at the molecular level.CORBA（国际对象管理协作组制定的使OOP对象与网络接口统一起来的一套跨计算机、操作系统、程序语言和网络的共同标准）The Common Object Request Broker Architecture (CORBA) is an open industry standard for working with distributed objects, developed by the Object Management Group. CORBA allows the interconnection of objects and applications regardless of computer language, machine architecture, or geographic location of the computers.Correlation coefficient（相关系数）A numerical measure, falling between - 1 and 1, of the degree of the linear relationship between two variables. A positive value indicates a direct relationship, a negative value indicates an inverse relationship, and the distance of the value away from zero indicates the strength of the relationship. A value near zero indicates no relationship between the variables.Covariation (in sequences)（共变）Coincident change at two or more sequence positions in related sequences that may influence the secondary structures of RNA or protein molecules.Coverage (or depth) （覆盖率/厚度）The average number of times a nucleotide is represented by a high-quality base in a collection of random raw sequence. Operationally, a 'high-quality base' is defined as one with an accuracy of at least 99% (corresponding to a PHRED score of at least 20).Database（数据库）A computerized storehouse of data that provides a standardized way for locating, adding, removing, and changing data. See also Object-oriented database, Relational database.DendogramA form of a tree that lists the compared objects (e.g., sequences or genes in a microarray analysis) in a vertical order and joins related ones by levels of branches extending to one side of the list.Depth （厚度）See coverageDirichlet mixturesDefined as the conjugational prior of a multinomial distribution. One use is for predicting the expected pattern of amino acid variation found in the match state of a hid-den Markov model (representing one column of a multiple sequence alignment of proteins), based on prior distributions found in conserved protein domains (blocks).Distance in sequence analysis（序列距离）The number of observed changes in an optimal alignment of two sequences, usually not counting gaps.DNA Sequencing （DNA测序）The experimental process of determining the nucleotide sequence of a region of DNA. This is done by labelling each nucleotide (A, C, G or T) with either a radioactive or fluorescent marker which identifies it. There are several methods of applying this technology, each with their advantages and disadvantages. For more information, refer to a current text book. High throughput laboratories frequently use automated sequencers, which are capable of rapidly reading large numbers of templates. Sometimes, the sequences may be generated more quickly than they can be characterised.Domain （功能域）A discrete portion of a protein assumed to fold independently of the rest of the protein andpossessing its own function.Dot matrix（点标矩阵图）Dot matrix diagrams provide a graphical method for comparing two sequences. One sequence is written horizontally across the top of the graph and the other along the left-hand side. Dots are placed within the graph at the intersection of the same letter appearing in both sequences. A series of diagonal lines in the graph indicate regions of alignment. The matrix may be filtered to reveal the most-alike regions by scoring a minimal threshold number of matches within a sequence window.Draft genome sequence （基因组序列草图）The sequence produced by combining the information from the individual sequenced clones (by creating merged sequence contigs and then employing linking information to create scaffolds) and positioning the sequence along the physical map of the chromosomes.DUST （一种低复杂性区段过滤程序）A program for filtering low complexity regions from nucleic acid sequences.Dynamic programming（动态规划法）A dynamic programming algorithm solves a problem by combining solutions to sub-problems that are computed once and saved in a table or matrix. Dynamic programming is typically used when a problem has many possible solutions and an optimal one needs to be found. This algorithm is used for producing sequence alignments, given a scoring system for sequence comparisons.EMBL （欧洲分子生物学实验室，EMBL数据库是主要公共核酸序列数据库之一）European Molecular Biology Laboratories. Maintain the EMBL database, one of the major public sequence databases.EMBnet （欧洲分子生物学网络）European Molecular Biology Network: /was established in 1988, and provides services including local molecular databases and software for molecular biologists in Europe. There are several large outposts of EMBnet, including EXPASY.Entropy（熵）From information theory, a measure of the unpredictable nature of a set of possible elements. The higher the level of variation within the set, the higher the entropy.Erdos and Renyi lawIn a toss of a “fair” coin, the number of heads in a row that can be expected is the logarithm of the number of tosses to the base 2. The law may be generalized for more than two possible outcomes by changing the base of the logarithm to the number of out-comes. This law was used to analyze the number of matches and mismatches that can be expected between random sequences as a basis for scoring the statistical significance of a sequence alignment.EST （表达序列标签的缩写）See Expressed Sequence TagExpect value (E)（E值）E value. The number of different alignents with scores equivalent to or better than S that are expected to occur in a database search by chance. The lower the E value, the more significant the score. In a database similarity search, the probability that an alignment score as good as the one found between a query sequence and a database sequence would be found in as many comparisons between random sequences as was done to find the matching sequence. In other types of sequence analysis, E has a similar meaning.Expectation maximization (sequence analysis)An algorithm for locating similar sequence patterns in a set of sequences. A guessed alignment of the sequences is first used to generate an expected scoring matrix representing the distribution of sequence characters in each column of the alignment, this pattern is matched to each sequence, and the scoring matrix values are then updated to maximize the alignment of the matrix to the sequences. The procedure is repeated until there is no further improvement.Exon （外显子）Coding region of DNA. See CDS.Expressed Sequence Tag (EST) （表达序列标签）Randomly selected, partial cDNA sequence; represents it's corresponding mRNA. dbEST is a large database of ESTs at GenBank, NCBI.FASTA （一种主要数据库搜索程序）The first widely used algorithm for database similarity searching. The program looks for optimal local alignments by scanning the sequence for small matches called "words". Initially, the scores of segments in which there are multiple word hits are calculated ("init1"). Later the scores of several segments may be summed to generate an "initn" score. An optimized alignment that includes gaps is shown in the output as "opt". The sensitivity and speed of the search are inversely related and controlled by the "k-tup" variable which specifies the size of a "word". (Pearson andLipman)Extreme value distribution（极值分布）Some measurements are found to follow a distribution that has a long tail which decays at high values much more slowly than that found in a normal distribution. This slow-falling type is called the extreme value distribution. The alignment scores between unrelated or random sequences are an example. These scores can reach very high values, particularly when a large number of comparisons are made, as in a database similarity search. The probability of a particular score may be accurately predicted by the extreme value distribution, which follows a double negative exponential function after Gumbel.False negative（假阴性）A negative data point collected in a data set that was incorrectly reported due to a failure of the test in avoiding negative results.False positive （假阳性）A positive data point collected in a data set that was incorrectly reported due to a failure of the test. If the test had correctly measured the data point, the data would have been recorded as negative.Feed-forward neural network （反向传输神经网络）Organizes nodes into sequence layers in which the nodes in each layer are fully connected with the nodes in the next layer, except for the final output layer. Input is fed from the input layer through the layers in sequence in a “feed-forward” direction, resulting in output at the final layer. See also Neural network.Filtering (window size)During pair-wise sequence alignment using the dot matrix method, random matches can be filtered out by using a sliding window to compare the two sequences. Rather than comparing a single sequence position at a time, a window of adjacent positions in the two sequences is compared and a dot, indicating a match, is generated only if a certain minimal number of matches occur.Filtering （过滤）Also known as Masking. The process of hiding regions of (nucleic acid or amino acid) sequence having characteristics that frequently lead to spurious high scores. See SEG and DUST.Finished sequence（完成序列）Complete sequence of a clone or genome, with an accuracy of at least 99.99% and no gaps.Fourier analysisStudies the approximations and decomposition of functions using trigonometric polynomials.Format (file)（格式）Different programs require that information be specified to them in a formal manner, using particular keywords and ordering. This specification is a file format.Forward-backward algorithmUsed to train a hidden Markov model by aligning the model with training sequences. The algorithm then refines the model to reduce the error when fitted to the given data using a gradient descent approach.FTP (File Transfer Protocol)（文件传输协议）Allows a person to transfer files from one computer to another across a network using an FTP-capable client program. The FTP client program can only communicate with machines that run an FTP server. The server, in turn, will make a specific portion of its tile system available for FTP access, providing that the client is able to supply a recognized user name and password to the server.Full shotgun clone （鸟枪法克隆）A large-insert clone for which full shotgun sequence has been produced.Functional genomics（功能基因组学）Assessment of the function of genes identified by between-genome comparisons. The function of a newly identified gene is tested by introducing mutations into the gene and then examining the resultant mutant organism for an altered phenotype.gap （空位/间隙/缺口）A space introduced into an alignment to compensate for insertions and deletions in one sequence relative to another. To prevent the accumulation of too many gaps in an alignment, introduction of a gap causes the deduction of a fixed amount (the gap score) from the alignment score. Extension of the gap to encompass additional nucleotides or amino acid is also penalized in the scoring of an alignment.Gap penalty（空位罚分）A numeric score used in sequence alignment programs to penalize the presence of gaps within an alignment. The value of a gap penalty affects how often gaps appear in alignments produced by the algorithm. Most alignment programs suggest gap penalties that are appropriate for particular scoring matrices.Genetic algorithm（遗传算法）A kind of search algorithm that was inspired by the principles of evolution. A population of initial solutions is encoded and the algorithm searches through these by applying a pre-defined fitness measurement to each solution, selecting those with the highest fitness for reproduction. New solutions can be generated during this phase by crossover and mutation operations, defined in the encoded solutions.Genetic map （遗传图谱）A genome map in which polymorphic loci are positioned relative to one another on the basis of the frequency with which they recombine during meiosis. The unit of distance is centimorgans (cM), denoting a 1% chance of recombination.Genome（基因组）The genetic material of an organism, contained in one haploid set of chromosomes.Gibbs sampling methodAn algorithm for finding conserved patterns within a set of related sequences. A guessed alignment of all but one sequence is made and used to generate a scoring matrix that represents the alignment. The matrix is then matched to the left-out sequence, and a probable location of the corresponding pattern is found. This prediction is then input into a new alignment and another scoring matrix is produced and tested on a new left-out sequence. The process is repeated until there is no further improvement in the matrix.Global alignment（整体联配）Attempts to match as many characters as possible, from end to end, in a set of twomore sequences.Gopher (一个文档发布系统，允许检索和显示文本文件)Graph theory（图论）A branch of mathematics which deals with problems that involve a graph or network structure. A graph is defined by a set of nodes (or points) and a set of arcs (lines or edges) joining the nodes. In sequence and genome analysis, graph theory is used for sequence alignments and clustering alike genes.GSS（基因综述序列）Genome survey sequence.GUI（图形用户界面）Graphical user interface.H （相对熵值）H is the relative entropy of the target and background residue frequencies. (Karlin and Altschul, 1990). H can be thought of as a measure of the average information (in bits) available per position that distinguishes an alignment from chance. At high values of H, short alignments can be distinguished by chance, whereas at lower H values, a longer alignment may be necessary. (Altschul, 1991)Half-bitsSome scoring matrices are in half-bit units. These units are logarithms to the base 2 of odds scores times 2.Heuristic（启发式方法）A procedure that progresses along empirical lines by using rules of thumb to reach a solution. The solution is not guaranteed to be optimal.Hexadecimal system（16制系统）The base 16 counting system that uses the digits O-9 followed by the letters A-F.HGMP （人类基因组图谱计划）Human Genome Mapping Project.Hidden Markov Model (HMM)（隐马尔可夫模型）In sequence analysis, a HMM is usually a probabilistic model of a multiple sequence alignment, but can also be a model of periodic patterns in a single sequence, representing, for example, patterns found in the exons of a gene. In a model of multiple sequence alignments, each column of symbols in the alignment is represented by a frequency distribution of the symbols called a state, and insertions and deletions by other states. One then moves through the model along a particular path from state to state trying to match a given sequence. The next matching symbol is chosen from each state, recording its probability (frequency) and also the probability of going to thatparticular state from a previous one (the transition probability). State and transition probabilities are then multiplied to obtain a probability of the given sequence. Generally speaking, a HMM is a statistical model for an ordered sequence of symbols, acting as a stochastic state machine that generates a symbol each time a transition is made from one state to the next. Transitions betweenstates are specified by transition probabilities.Hidden layer（隐藏层）An inner layer within a neural network that receives its input and sends its output to other layers within the network. One function of the hidden layer is to detect covariation within the input data, such as patterns of amino acid covariation that are associated with a particular type of secondary structure in proteins.Hierarchical clustering（分级聚类）The clustering or grouping of objects based on some single criterion of similarity or difference.An example is the clustering of genes in a microarray experiment based on the correlation between their expression patterns. The distance method used in phylogenetic analysis is another example.Hill climbingA nonoptimal search algorithm that selects the singular best possible solution at a given state or step. The solution may result in a locally best solution that is not a globally best solution.Homology（同源性）A similar component in two organisms (e.g., genes with strongly similar sequences) that can be attributed to a common ancestor of the two organisms during evolution.Horizontal transfer（水平转移）The transfer of genetic material between two distinct species that do not ordinarily exchange genetic material. The transferred DNA becomes established in the recipient genome and can be detected by a novel phylogenetic history and codon content com-pared to the rest of the genome.HSP （高比值片段对）High-scoring segment pair. Local alignments with no gaps that achieve one of the top alignment scores in a given search.HTGS/HGT（高通量基因组序列）High-throughout genome sequences。
生物信息学考试参考题目
1. 在NCBI进行BLAST序列比对时，需要输入查询序列的信息，以下错误的格式是（ C ）A. 序列的accession numberB. 序列的giC. 序列对应基因的IDD. FASTA 格式的序列2. 下面这段序列是: ( B )>gi|24646620|ref|NM_057587.3| Drosophila melanogaster RNA-binding protein 4 CG9654-RA, transcript variant A (Rbp4), mRNAGGATTTTCTTGCCTGTCA TTCAA TTTGTGGTTGGCTTCACCTGAGTGCTGTAGT。
A. DNA序列B. RNA序列C. 蛋白质序列D. 基因3. ExPASy上的工具软件ProtParam提供的是哪种类型的服务？（ B ）A．蛋白质三级结构分析B．蛋白质序列理化性质预测C．蛋白质二级结构分析D．跨膜结构分析4. 假如你有两条远相关的蛋白，为了比较它们，最好使用下列哪个记分矩阵（A ）A. BLOSUM45或PAM250B. BLOSUM45或PAM1C. BLOSUM80或PAM250D. BLOSUM10或PAM15. 构建系统发生树，应使用CA. BLASTB. FASTAC. UPGMAD. Entrez6. 下面这段蛋白质序列是什么格式? ( D )>gi|4506183|ref|NP_002779.1| proteasome alpha 3 [Homo sapiens]MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLS KL YEEGSNKRLFNVDRHVGMA V AGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRV AMYVHAYTL YSA VRPFGCSFMLGS。
A. GBFFB. TEXTC. PDBD. FASTA7. 直系同源物定义为（A ）A．不同物种中具有共同祖先的同源序列B．具有较小的氨基酸一致性但是有较大的结构相似性的同源序列C．同一物种中由基因复制产生的同源序列D．同一物种中具有相似的并且通常是冗余功能的同源序列8. 美国NIH维护提供的DNA序列数据库是：（ A ）A. GenBankB. ProteinC. dbESTD. dbSNP9. 高分配对片段的英文缩写为（A ）A. HSPB. HMPC. HCPD. HDP10. BLAST比对结果报告中有一统计数值E值，该值大小与匹配度的关系是（ B ）A. 值越小说明匹配度越低B. 值越小说明匹配度越高C. 两者无内在关系D. 以上说法都不对11. NCBI提供了大量的序列分析工具，其中用来寻找DNA序列潜在的蛋白质编码区的工具是：（A ）A. ORF FinderB. BLASTC. Scan PrositeD. SAGEmap12. Entrez是哪个网站数据库的检索系统（A ）A．NCBIB．PROSITEC．EBID．PDB13. 如果想找一个和查询蛋白远源的蛋白质，下面哪种方法最可能成功？ BA．采用PHI-BLAST，因为你能自己选择一个和搜索蛋白质有关的信号序列B．采用PSI-BLAST，因为这个算法使用位点特异性打分矩阵最为敏感C．采用BLASTP，因为你能够调整你的打分矩阵从而使得搜索敏感度最大D．采用专门的物种数据库，因为他们中可能含有这种远源序列。
生物信息学主要英文术语及释义
生物信息学主要英文术语及释义生物信息学主要英文术语及释义Abstract Abstract Syntax Syntax Syntax Notation Notation Notation (ASN.l)(ASN.l)（NCBI 发展的许多程序，如显示蛋白质三维结构的Cn3D等所使用的内部格式）等所使用的内部格式） A A language language language that that that is is is used used used to to to describe describe describe structured structured structured data data data types types types formally, formally, formally, Within Within Within bioinformatits,it bioinformatits,it bioinformatits,it has has been been used used used by by by the the the National National National Center Center Center for for for Biotechnology Biotechnology Biotechnology Information Information Information to to to encode encode encode sequences, sequences, sequences, maps, maps, taxonomic information, molecular structures, and biographical information in such a way that it can be easily accessed and exchanged by computer software. Accession number （记录号）（记录号）A unique identifier that is assigned to a single database entry for a DNA or protein sequence. Affine gap penalty （一种设置空位罚分策略）（一种设置空位罚分策略）（一种设置空位罚分策略） A gap penalty score that is a linear function of gap length, consisting of a gap opening penalty and a a gap gap gap extension extension extension penalty penalty penalty multiplied multiplied multiplied by by by the the the length length length of of of the the the gap. gap. gap. Using Using Using this this this penalty penalty penalty scheme scheme scheme greatly greatly enhances enhances the the the performance performance performance of of of dynamic dynamic dynamic programming programming programming methods methods methods for for for sequence sequence sequence alignment. alignment. alignment. See See See also also Gap penalty. Algorithm （算法）（算法）A A systematic systematic systematic procedure procedure procedure for solving for solving a a problem problem problem in in in a a a finite finite finite number number number of of of steps, steps, steps, typically typically typically involving involving involving a a repetition of operations. Once specified, an algorithm can be written in a computer language and run as a program. Alignment （联配/比对/联配）联配）Refers to the procedure of comparing two or more sequences by looking for a series of individual characters or character patterns that are in the same order in the sequences. Of the two types of alignment, alignment, local local local and and and global, global, global, a a a local local local alignment alignment alignment is is is generally generally generally the the the most most most useful. useful. useful. See See See also also also Local Local Local and and Global alignments. Alignment score （联配/比对/联配值）联配值）An algorithmically computed score based on the number of matches, substitutions, insertions, and deletions deletions (gaps) (gaps) (gaps) within within within an an an alignment. alignment. alignment. Scores Scores Scores for for for matches matches matches and and and substitutions substitutions substitutions Are Are Are derived derived derived from from from a a scoring scoring matrix matrix matrix such such such as as as the the the BLOSUM BLOSUM BLOSUM and and and P AM P AM matrices matrices matrices for for for proteins, proteins, proteins, and and and aftine aftine aftine gap gap gap penalties penalties suitable for the matrix are chosen. Alignment scores are in log odds units, often bit units (log to the the base base base 2). 2). 2). Higher Higher Higher scores scores scores denote denote denote better better better alignments. alignments. alignments. See See See also also also Similarity Similarity Similarity score, score, score, Distance Distance Distance in in sequence analysis. Alphabet （字母表）（字母表）The total number of symbols in a sequence-4 for DNA sequences and 20 for protein sequences. Annotation （注释）（注释）The The prediction prediction prediction of of of genes genes genes in in in a a a genome, genome, genome, including including including the the the location location location of of of protein-encoding protein-encoding protein-encoding genes, genes, genes, the the sequence of the encoded proteins, anysignificantmatches to other Proteins of known function, and the location of RNA-encoding genes. Predictions are based on gene models; e.g., hidden Markov models models of of of introns introns introns and and and exons exons exons in in in proteins proteins proteins encoding encoding encoding genes, genes, genes, and and and models models models of of of secondary secondary secondary structure structure structure in in RNA. Anonymous FTP （匿名FTP ）When a FTP service allows anyone to log in, it is said to provide anonymous FTP ser-vice. A user can can log log log in in in to to to an an an anonymous anonymous anonymous FTP FTP FTP server server server by by by typing typing typing anonymous anonymous anonymous as as the the user name user name and and his E-mail his E-mail address as a password. Most Web browsers now negotiate anonymous FTP logon without asking the user for a user name and password. See also FTP. ASCII The American Standard Code for Information Interchange (ASCII) encodes unaccented letters a-z, A-Z, A-Z, the the the numbers numbers numbers O-9, O-9, O-9, most most most punctuation punctuation punctuation marks, marks, marks, space, space, space, and and and a a a set set set of of of control control control characters characters characters such such such as as carriage carriage return return return and and and tab. tab. tab. ASCII ASCII ASCII specifies specifies specifies 128 128 128 characters characters characters that that that are are are mapped mapped mapped to to to the the the values values values O-127. O-127. ASCII ASCII tiles tiles tiles are are are commonly commonly commonly called called called plain plain plain text, text, text, meaning meaning meaning that that that they they they only only only encode encode encode text text text without without without extra extra markup. BAC clone （细菌人工染色体克隆）（细菌人工染色体克隆）Bacterial Bacterial artificial artificial artificial chromosome chromosome chromosome vector vector vector carrying carrying carrying a a a genomic genomic genomic DNA DNA DNA insert, insert, insert, typically typically typically 100100100––200 200 kb. kb. Most of the large-insert clones sequenced in the project were BAC clones. Back-propagation （反向传输）（反向传输）When training feed-forward neural networks, a back-propagation algorithm can be used to modify the network weights. After each training input pattern is fed through the network, the network’s output output is is is compared compared compared with with with the the the desired desired desired output output output and and and the the the amount amount amount of of of error error error is is is calculated. calculated. calculated. This This This error error error is is back-propagated through the network by using an error function to correct the network weights. See also Feed-forward neural network. Baum-Welch algorithm （Baum-Welch 算法）算法）An expectation maximization algorithm that is used to train hidden Markov models. Baye ’s rule （贝叶斯法则）（贝叶斯法则）Forms Forms the the the basis basis basis of of of conditional conditional conditional probability probability probability by by by calculating calculating calculating the the the likelihood likelihood likelihood of of of an an an event event event occurring occurring based on the history of the event and relevant background information. In terms of two parameters A and B, the theorem is stated in an equation: The condition-al probability of A, given B, P(AIB), is is equal equal equal to to to the the the probability probability probability of of of A, P(A), A, P(A), times times the the the conditional conditional conditional probability probability probability of of of B, B, B, given given given A, P(BIA), A, P(BIA), divided by the probability of B, P(B). P(A) is the historical or prior distribution value of A, P(BIA) is a new prediction for B for a particular value of A, and P(B) is the sum of the newly predicted values for B. P(AIB) is a posterior probability, representing a new prediction for A given the prior knowledge of A and the newly discovered relationships between A and B. Bayesian analysis （贝叶斯分析）（贝叶斯分析）A A statistical statistical statistical procedure procedure procedure used used used to to to estimate estimate estimate parameters parameters parameters of of of an an an underlyingdistribution underlyingdistribution underlyingdistribution based based based on on on an an observed distribution. See a lso Baye’s rule.Biochips （生物芯片）（生物芯片）Miniaturized arrays of large numbers of molecular substrates, often oligonucleotides, in a defined pattern. They are also called DNA microarrays and microchips. Bioinformatics （生物信息学）（生物信息学）The merger of biotechnology and information technology with the goal of revealing new insights and and principles principles principles in in in biology. biology. biology. /The /The /The discipline discipline discipline of of of obtaining obtaining obtaining information information information about about about genomic genomic genomic or or or protein protein sequence sequence data. data. data. This This This may may may involve involve involve similarity similarity similarity searches searches searches of of of databases, databases, databases, comparing comparing comparing your your your unidentified unidentified sequence sequence to to to the the the sequences sequences sequences in in in a a a database, database, database, or or or making making making predictions predictions predictions about about about the the the sequence sequence sequence based based based on on current current knowledge knowledge knowledge of of of similar similar similar sequences. sequences. sequences. Databases Databases Databases are are are frequently frequently frequently made made made publically publically publically available available through the Internet, or locally at your institution. Bit score （二进制值/ Bit 值）值）The value S' is derived from the raw alignment score S in which the statistical properties of the scoring system used have been taken into account. Because bit scores have been normalized with respect respect to to to the the the scoring scoring scoring system, system, system, they they they can can can be be be used used used to to to compare compare compare alignment alignment alignment scores scores scores from from from different different searches. Bit units From information theory, a bit denotes the amount of information required to distinguish between two two equally equally equally likely likely likely possibilities. possibilities. possibilities. The The The number number number of of of bits bits bits of of of information, information, information, AJ, AJ, AJ, required required required to to to convey convey convey a a message that has A4 possibilities is log2 M = N bits. BLAST （基本局部联配搜索工具，一种主要数据库搜索程序）（基本局部联配搜索工具，一种主要数据库搜索程序）Basic Local Alignment Search Tool. A set of programs, used to perform fast similarity searches. Nucleotide sequences can be compared with nucleotide sequences in a database using BLASTN, for for example. example. example. Complex Complex Complex statistics statistics statistics are are are applied applied applied to to to judge judge judge the the the significance significance significance of of of each each each match. match. match. Reported Reported sequences may be homologous to, or related to the query sequence. The BLASTP program is used to search a protein database for a match against a query protein sequence. There are several other flavours of BLAST. BLAST2 is a newer release of BLAST. Allows for insertions or deletions in the sequences being aligned. Gapped alignments may be more biologically significant. Block （蛋白质家族中保守区域的组块）（蛋白质家族中保守区域的组块）Conserved Conserved ungapped ungapped ungapped patterns patterns patterns approximately approximately approximately 3-60 3-60 3-60 amino amino amino acids acids acids in in in length length length in in in a a a set set set of of of related related proteins. BLOSUM matrices （模块替换矩阵，一种主要替换矩阵）（模块替换矩阵，一种主要替换矩阵）An alternative to PAM tables, BLOSUM tables were derived using local multiple alignments of more distantly related sequences than were used for the PAM matrix. These are used to assess the similarity of sequences when performing alignments. Boltzmann distribution （Boltzmann 分布）分布）Describes Describes the the the number number number of of of molecules molecules molecules that that that have have have energies energies energies above above above a a a certain certain certain level, level, level, based based based on on on the the Boltzmann gas constant and the absolute temperature.Boltzmann probability function(Boltzmann 概率函数) See Boltzmann distribution. Bootstrap analysis A method for testing how well a particular data set fits a model. For example, the validity of the branch branch arrangement arrangement arrangement in in in a a a predicted predicted predicted phylogenetic phylogenetic phylogenetic tree tree tree can can can be be be tested tested tested by by by resampling resampling resampling columns columns columns in in in a a multiple multiple sequence sequence sequence alignment alignment alignment to to to create create create many many many new new new alignments. alignments. alignments. The The The appearance appearance appearance of of of a a a particular particular branch in trees generated from these resampled sequences can then be measured. Alternatively, a sequence sequence may may may be be be left left left out out out of of of an an an analysis analysis analysis to to to deter-mine deter-mine deter-mine how how how much much much the the the sequence sequence sequence influences influences influences the the results of an analysis. Branch length （分支长度）（分支长度）In sequence analysis, the number of sequence changes along a particular branch of a phylogenetic tree. CDS or cds （编码序列）（编码序列）（编码序列） Coding sequence. Chebyshe, d inequality The probability that a random variable exceeds its mean is less than or equal to the square of 1 over the number of standard deviations from the mean. Clone （克隆）（克隆）Population of identical cells or molecules (e.g. DNA), derived from a single ancestor. Cloning V ector （克隆载体）（克隆载体）A molecule that carries a foreign gene into a host, and allows/facilitates the multiplication of that gene in a host. When sequencing a gene that has been cloned using a cloning vector (rather than by by PCR), PCR), PCR), care care care should should should be be be taken taken taken not not not to to to include include include the the the cloning cloning cloning vector vector vector sequence sequence sequence when when when performing performing similarity searches. Plasmids, cosmids, phagemids, Y ACs and PACs are example types of cloning vectors. Cluster analysis （聚类分析）（聚类分析） A method for grouping together a set of objects that are most similar from a larger group of related objects. The relationships are based on some criterion of similarity or difference. For sequences, a similarity or distance score or a statistical evaluation of those scores is used. Cobbler A single sequence that represents the most conserved regions in a multiple sequence alignment. The BLOCKS server uses the cobbler sequence to perform a database similarity search as a way to reach sequences that are more divergent than would be found using the single sequences in the alignment for searches. Coding system (neural networks) Regarding Regarding neural neural neural networks, networks, networks, a a a coding coding coding system system system needs needs needs to to to be be be designed designed designed for for for representing representing representing input input input and and output. output. The The The level level level of of of success success success found found found when when when training training training the the the model model model will will will be be be partially partially partially dependent dependent dependent on on on the the quality of the coding system chosen. Codon usageAnalysis of the codons used in a particular gene or organism. COG （直系同源簇）（直系同源簇）Clusters of orthologous groups in a set of groups of related sequences in microorganism and yeast (S. cerevisiae). These groups are found by whole proteome comparisons and include orthologs and paralogs. See also Orthologs and Paralogs. Comparative genomics （比较基因组学）（比较基因组学）A comparison of gene numbers, gene locations, and biological functions of genes in the genomes of diverse organisms, one objective being to identify groups of genes that play a unique biological role in a particular organism. Complexity (of an algorithm)（算法的复杂性）（算法的复杂性）Describes the number of steps required by the algorithm to solve a problem as a function of the amount of data; for example, the length of sequences to be aligned. Conditional probability （条件概率）（条件概率）The The probability probability probability of of of a a a particular particular particular result result result (or (or (or of of of a a a particular particular particular value value value of of of a a a variable) variable) variable) given given given one one one or or or more more events or conditions (or values of other variables). Conservation （保守）（保守）Changes at a specific position of an amino acid or (less commonly, DNA) sequence that preserve the physico-chemical properties of the original residue. Consensus （一致序列）（一致序列）A A single single single sequence sequence sequence that that that represents, represents, represents, at at at each each each subsequent subsequent subsequent position, position, position, the the the variation variation variation found found found within within corresponding columns of a multiple sequence alignment. Context-free grammars A A recursive recursive recursive set set set of of of production production production rules rules rules for for for generating generating generating patterns patterns patterns of of of strings. strings. strings. These These These consist consist consist of of of a a a set set set of of terminal characters that are used to create strings, a set of nonterminal symbols that correspond to rules and act as placeholders for patterns that can be generated using terminal characters, a set of rules for replacing nonterminal symbols with terminal characters, and a start symbol. Contig （序列重叠群/拼接序列）拼接序列）A A set set set of of of clones clones clones that that that can can can be be be assembled assembled assembled into into into a a a linear linear linear order. order. order. A A A DNA DNA DNA sequence sequence sequence that that that overlaps overlaps overlaps with with another contig. The full set of overlapping sequences (contigs) can be put together to obtain the sequence for a long region of DNA that cannot be sequenced in one run in a sequencing assay. Important in genetic mapping at the molecular level. CORBA （国际对象管理协作组制定的使OOP 对象与网络接口统一起来的一套跨计算机、操作系统、程序语言和网络的共同标准）作系统、程序语言和网络的共同标准）The The Common Common Common Object Object Object Request Request Request Broker Broker Broker Architecture Architecture Architecture (CORBA) (CORBA) (CORBA) is is is an an an open open open industry industry industry standard standard standard for for working working with with with distributed distributed distributed objects, objects, objects, developed developed developed by by by the the the Object Object Object Management Management Management Group. CORBA allows Group. CORBA allows the interconnection of objects and applications regardless of computer language, machine architecture, or geographic location of the computers. Correlation coefficient （相关系数）（相关系数）A numerical measure, falling between - 1 and 1, of the degree of the linear relationship between two variables. A positive value indicates a direct relationship, a negative negative value value value indicates indicates indicates an an an inverse inverse inverse relationship, relationship, relationship, and and and the the the distance distance distance of of of the the the value value value away away away from from from zero zero indicates the strength of the relationship. A value near zero indicates no relationship between the variables. Covariation (in sequences)（共变）（共变）Coincident change at two or more sequence positions in related sequences that may influence the secondary structures of RNA or protein molecules. Coverage (or depth) （覆盖率（覆盖率/厚度）厚度）The average number of times a nucleotide is represented by a high-quality base in a collection of random raw sequence. Operationally, a 'high-quality base' is defined as one with an accuracy of at least 99% (corresponding to a PHRED score of at least 20). Database （数据库）（数据库）A A computerized computerized computerized storehouse storehouse storehouse of of of data data data that that that provides provides provides a a a standardized standardized standardized way way way for for for locating, locating, locating, adding, adding, removing, and changing data. See also Object-oriented database, Relational database. Dendogram A form of a tree that lists the compared objects (e.g., sequences or genes in a microarray analysis) in a vertical order and joins related ones by levels of branches extending to one side of the list. Depth （厚度）（厚度）See coverage Dirichlet mixtures Defined Defined as as as the the the conjugational conjugational conjugational prior prior prior of of of a a a multinomial multinomial multinomial distribution. distribution. distribution. One One One use use use is is is for for for predicting predicting predicting the the expected expected pattern pattern pattern of of of amino amino amino acid acid acid variation variation variation found found found in in in the the the match match match state state state of of of a a a hid-den hid-den hid-den Markov Markov Markov model model (representing one column of a multiple sequence alignment of proteins), based on prior distributions found in conserved protein domains (blocks). Distance in sequence analysis （序列距离）（序列距离）The number of observed changes in an optimal alignment of two sequences, usually not counting gaps. DNA Sequencing （DNA 测序）测序）The The experimental experimental experimental process process process of of of determining determining determining the the the nucleotide nucleotide nucleotide sequence sequence sequence of of of a a a region region region of of of DNA. DNA. DNA. This This This is is done by labelling each nucleotide (A, C, G or T) with either a radioactive or fluorescent marker which which identifies identifies identifies it. it. it. There There There are are are several several several methods methods methods of of of applying applying applying this this this technology, technology, each each with with with their their advantages and disadvantages. For more information, refer to a current text book. High throughput laboratories laboratories frequently frequently frequently use use use automated automated automated sequencers, sequencers, sequencers, which which which are are are capable capable capable of of of rapidly rapidly rapidly reading reading reading large large numbers of templates. Sometimes, the sequences may be generated more quickly than they can be characterised. Domain （功能域）（功能域）A A discrete discrete discrete portion portion portion of of of a a a protein protein protein assumed assumed assumed to to to fold fold fold independently independently independently of of of the the the rest rest rest of of of the the the protein protein protein and and possessing its own function.Dot matrix （点标矩阵图）（点标矩阵图）Dot matrix diagrams provide a graphical method for comparing two sequences. One sequence is written horizontally across the top of the graph and the other along the left-hand side. Dots are placed within the graph at the intersection of the same letter appearing in both sequences. A series of diagonal lines in the graph indicate regions of alignment. The matrix may be filtered to reveal the the most-alike most-alike most-alike regions regions regions by by by scoring scoring scoring a a a minimal minimal minimal threshold threshold threshold number number number of of of matches matches matches within within within a a a sequence sequence window. Draft genome sequence （基因组序列草图）（基因组序列草图）（基因组序列草图） The sequence produced by combining the information from the individual sequenced clones (by creating merged sequence contigs and then employing linking information to create scaffolds) and positioning the sequence along the physical map of the chromosomes. DUST （一种低复杂性区段过滤程序）（一种低复杂性区段过滤程序）A program for filtering low complexity regions from nucleic acid sequences. Dynamic programming （动态规划法）（动态规划法）A dynamic programming algorithm solves a problem by combining solutions to sub-problems that are computed once and saved in a table or matrix. Dynamic programming is typically used when a problem has many possible solutions and an optimal one needs to be found. This algorithm is used for producing sequence alignments, given a scoring system for sequence comparisons. EMBL （欧洲分子生物学实验室，EMBL 数据库是主要公共核酸序列数据库之一）数据库是主要公共核酸序列数据库之一）European Molecular Biology Laboratories. Maintain the EMBL database, one of the major public sequence databases. EMBnet （欧洲分子生物学网络）（欧洲分子生物学网络）European European Molecular Molecular Molecular Biology Biology Biology Network: Network: Network: / / was was established established established in in in 1988, 1988, 1988, and and provides provides services services services including including including local local local molecular molecular molecular databases databases databases and and and software software software for for for molecular molecular molecular biologists biologists biologists in in Europe. There are several large outposts of EMBnet, including EXPASY . Entropy （熵）（熵）From information theory, a measure of the unpredictable nature of a set of possible elements. The higher the level of variation within the set, the higher the entropy. Erdos and Renyi law In a toss of a “fair” coin, the number of heads in a row that can be expected is the logarithm of the number of tosses to the base 2. The law may be generalized for more than two possible outcomes by changing the base of the logarithm to the number of out-comes. This law was used to analyze the number of matches and mismatches that can be expected between random sequences as a basis for scoring the statistical significance of a sequence alignment. EST （表达序列标签的缩写）（表达序列标签的缩写）See Expressed Sequence Tag Expect value (E)（E 值）值）E E value. value. value. The The The number number number of of of different different different alignents alignents alignents with with with scores scores scores equivalent equivalent equivalent to to to or or or better better better than than than S S S that that that are are expected to occur in a database search by chance. The lower the E value, the more significant the score. In a database similarity search, the probability that an alignment score as good as the one found between a query sequence and a database sequence would be found in as many comparisons between random sequences as was done to find the matching sequence. In other types of sequence analysis, E has a similar meaning. Expectation maximization (sequence analysis) An algorithm for locating similar sequence patterns in a set of sequences. A guessed alignment of the sequences is first used to generate an expected scoring matrix representing the distribution of sequence characters in each column of the alignment, this pattern is matched to each sequence, and and the the the scoring scoring scoring matrix matrix matrix values values values are are are then then then updated updated updated to to to maximize maximize maximize the the the alignment alignment alignment of of of the the the matrix matrix matrix to to to the the sequences. The procedure is repeated until there is no further improvement. Exon （外显子）（外显子）。
2012生物信息学复习题
2012生物信息学复习题一、选择题1. 根据PAM打分矩阵，下列哪个氨基酸最不容易突变？A) 丙氨酸 B) 谷氨酰胺 C) 甲硫氨酸 D) 半胱氨酸2. 下列哪个句子最好描述了两序列全局比对和局部比对的不同？A) 全局比对通常用于DNA序列，而局部比对通常用于蛋白质序列；B) 全局比对允许间隙，而局部比对不允许间隙；C) 全局比对寻求全局最大化，而局部比对寻求局部最大化；D) 全局比对比对整条序列，而局部比对寻找最佳匹配子序列3. 与PAM打分矩阵比较，BLOSUM打分矩阵的最大区别在哪里？A) 它最好用于比对相关性很近的序列； B) 它是基于近相关蛋白的全局多序列比对；C) 它是基于远相关蛋白的局部多序列比对； D) 它结合了局部和全局比对信息4. 全局比对算法（如Needleman-Wunsch算法）是这样一种算法：A) 把两条比较的蛋白质放到一个矩阵中，然后通过穷尽搜索每一个可能的比对组合来寻找最佳分值的比对；B) 把两条比较的蛋白质放到一个矩阵中，然后通过迭代递归的方法找到最佳的分值；C) 把两条比较的蛋白质放到一个矩阵中，然后通过寻找最佳子序列的方法来找到最佳的比对；D) 能用于蛋白质，但不能用于DNA序列5. 数据库搜索中或双序列比对中，敏感性定义为：A) 搜索算法寻找真阳性（即同源序列）和避免假阳性（即不相干序列，但具有高相似分值）的能力；B) 搜索算法寻找真阳性（即同源序列）和避免假阳性（即没有被搜索算法报告的同源序列）的能力；C) 搜索算法寻找真阳性（即同源序列）和避免假阴性（即不相干序列，但具有高相似分值）的能力；D ) 搜索算法寻找真阳性（即同源序列）和避免假阴性（即没有被搜索算法报告的同源序列）的能力；6. 如有一小段DNA序列，基本上它能编码多少种蛋白？A）1 B）2 C）3 D）67. 有一段DNA序列，如想知道在主要的蛋白质数据库中哪一个与该DNA编码的蛋白最接近，你会选择用哪一个程序？A）blastn B）blastp C）blastx D）tblastx E）tblastn8. blast检索的哪一种输出估计了假阳性的数目？A）E值 B）Bit score C）Percent identity D）Percent positives9. 将下面哪个blast参数改变后会得到更少的检索结果？A）关闭low-complexity filter B）将期望值从1变为0C）提高极限值 D）将打分矩阵从PAM30改为PAM7010.极值分布A）描述了对数据库的query的scores的分布 B）比正态分布的总面积大C）对称 D）形状可用两个参数来描述，即 µ（平均值）和 λ（衰减系数）11.当blast检索的E值减小时A）K值也减小 B）score变大 C）概率p值变大 D）极值分布偏斜率减小12.标准化的blast score（也称为bit scores）A）是没有单位 B）可在不同的blast检索之间比较，即使使用了不同的打分矩阵C）与使用的打分矩阵无关 D）可在不同的blast检索之间比较，但前提是使用相同的打分矩阵13.在EMBL和NCBI数据库中未加工的DNA序列（与注释序列相比）是A）完全重叠了 B）很大程度上重叠了，不过序列不同 C）相对只有一点重叠14.下面的哪种工作，PSI-BLAST搜索最为有效A）在老鼠中找一个人类蛋白质的同源蛋白 B）在数据库查询中找到更多的匹配蛋白 C）在数据库查询中找到更多的匹配DNA序列 D）用模式序列或者信号序列加强数据库搜索15.下面的哪种blast程序是用氨基酸的信号序列在一个蛋白质家族中寻找匹配的？A）PSI-BLAST B）PHI-BLAST C）MS BLAST D）WormBLAST16.下面的哪种blast 程序用来分析免疫球蛋白最好？A）RPS-BLAST B）PHI-BLAST C）IgBLAST D）ProDom17.在一个位点特异性打分矩阵中，列中可以有20种氨基酸。
大基因组数据与生物信息学英文及翻译
Big Genomic Data in Bioinformatics CloudAbstractThe achievement of Human Genome project has led to the proliferation of genomic sequencing data. This along with the next generation sequencing has helped to reduce the cost of sequencing, which has further increased the demand of analysis of this large genomic data. This data set and its processing has aided medical researches.Thus, we require expertise to deal with biological big data. The concept of cloud computing and big data technologies such as the Apache Hadoop project, are hereby needed to store, handle and analyse this data. Because, these technologies provide distributed and parallelized data processing and are efficient to analyse even petabyte (PB) scale data sets. However, there are some demerits too which may include need of larger time to transfer data and lesser network bandwidth, majorly.人类基因组计划的实现导致基因组测序数据的增殖。
生物信息学英文介绍
生物信息学英文介绍Introduction to Bioinformatics.Bioinformatics is an interdisciplinary field that combines biology, computer science, mathematics, statistics, and other disciplines to analyze and interpret biological data. At its core, bioinformatics leverages computational tools and algorithms to process, manage, and minebiological information, enabling a deeper understanding of the molecular basis of life and its diverse phenomena.The field of bioinformatics has exploded in recent years, driven by the exponential growth of biological data generated by high-throughput sequencing technologies, proteomics, genomics, and other omics approaches. This data deluge has presented both challenges and opportunities for researchers. On one hand, the sheer volume and complexityof the data require sophisticated computational methods for analysis. On the other hand, the wealth of information contained within these data holds the promise oftransformative insights into the functions, interactions, and evolution of biological systems.The core tasks of bioinformatics encompass genome annotation, sequence alignment and comparison, gene expression analysis, protein structure prediction and function annotation, and the integration of multi-omic data. These tasks require a range of computational tools and algorithms, often developed by bioinformatics experts in collaboration with biologists and other researchers.Genome annotation, for example, involves the identification of genes and other genetic elements within a genome and the prediction of their functions. This process involves the use of bioinformatics algorithms to identify protein-coding genes, non-coding RNAs, and regulatory elements based on sequence patterns and other features. The resulting annotations provide a foundation forunderstanding the genetic basis of traits and diseases.Sequence alignment and comparison are crucial for understanding the evolutionary relationships betweenspecies and for identifying conserved regions within genomes. Bioinformatics algorithms, such as BLAST and multiple sequence alignment tools, are widely used for these purposes. These algorithms enable researchers to compare sequences quickly and accurately, revealing patterns of conservation and divergence that inform our understanding of biological diversity and function.Gene expression analysis is another key area of bioinformatics. It involves the quantification of thelevels of mRNAs, proteins, and other molecules within cells and tissues, and the interpretation of these data to understand the regulation of gene expression and its impact on cellular phenotypes. Bioinformatics tools and algorithms are essential for processing and analyzing the vast amounts of data generated by high-throughput sequencing and other experimental techniques.Protein structure prediction and function annotation are also important areas of bioinformatics. The structure of a protein determines its function, and bioinformatics methods can help predict the three-dimensional structure ofa protein based on its amino acid sequence. These predictions can then be used to infer the protein'sfunction and to understand how it interacts with other molecules within the cell.The integration of multi-omic data is a rapidly emerging area of bioinformatics. It involves theintegration and analysis of data from different omics platforms, such as genomics, transcriptomics, proteomics, and metabolomics. This approach enables researchers to understand the interconnectedness of different biological processes and to identify complex relationships between genes, proteins, and metabolites.In addition to these core tasks, bioinformatics also plays a crucial role in translational research and personalized medicine. It enables the identification of disease-associated genes and the development of targeted therapeutics. By analyzing genetic and other biological data from patients, bioinformatics can help predict disease outcomes and guide treatment decisions.The future of bioinformatics is bright. With the continued development of high-throughput sequencing technologies and other omics approaches, the amount of biological data available for analysis will continue to grow. This will drive the need for more sophisticated computational methods and algorithms to process and interpret these data. At the same time, the integration of bioinformatics with other disciplines, such as artificial intelligence and machine learning, will open up new possibilities for understanding the complex systems that underlie life.In conclusion, bioinformatics is an essential field for understanding the molecular basis of life and its diverse phenomena. It leverages computational tools and algorithms to process, manage, and mine biological information, enabling a deeper understanding of the functions, interactions, and evolution of biological systems. As the amount of biological data continues to grow, the role of bioinformatics in research and medicine will become increasingly important.。
生物信息学,英文
生物信息学,英文BioinformaticsBioinformatics is a rapidly growing field that combines biology, computer science, and information technology to analyze and interpret biological data. It has become an essential tool in modern scientific research, particularly in the fields of genomics, proteomics, and molecular biology. The advent of high-throughput sequencing technologies has led to an exponential increase in the amount of biological data available, and bioinformatics provides the means to manage, analyze, and interpret this vast amount of information.At its core, bioinformatics involves the use of computational methods and algorithms to store, retrieve, organize, analyze, and interpret biological data. This includes tasks such as DNA and protein sequence analysis, gene and protein structure prediction, and the identification of functional relationships between different biological molecules. Bioinformatics also plays a crucial role in the development of new drugs, the understanding of disease mechanisms, and the study of evolutionary processes.One of the primary applications of bioinformatics is in the field ofgenomics, where it is used to analyze and interpret DNA sequence data. Researchers can use bioinformatics tools to identify genes, predict their function, and study the genetic variation within and between species. This information is essential for understanding the genetic basis of diseases, developing personalized medicine, and exploring the evolutionary history of different organisms.In addition to genomics, bioinformatics is also widely used in proteomics, the study of the structure and function of proteins. Bioinformatics tools can be used to predict the three-dimensional structure of proteins, identify protein-protein interactions, and study the role of proteins in biological processes. This information is crucial for understanding the mechanisms of disease, developing new drugs, and engineering proteins for industrial and medical applications.Another important application of bioinformatics is in the field of systems biology, which aims to understand the complex interactions and relationships between different biological components within a living organism. By using computational models and simulations, bioinformaticians can study how these components work together to produce the observed behavior of a biological system. This knowledge can be used to develop new treatments for diseases, optimize agricultural practices, and gain a deeper understanding of the fundamental principles of life.Bioinformatics is also playing a crucial role in the field of personalized medicine, where the goal is to tailor medical treatments to the unique genetic and molecular profile of each individual patient. By using bioinformatics tools to analyze a patient's genetic and molecular data, healthcare providers can identify the most effective treatments and predict the likelihood of adverse reactions to certain drugs. This approach has the potential to improve patient outcomes, reduce healthcare costs, and pave the way for more targeted and effective therapies.In addition to its scientific applications, bioinformatics is also having a significant impact on various industries, such as agriculture, environmental science, and forensics. In agriculture, bioinformatics is used to improve crop yields, develop new pest-resistant varieties, and optimize the use of resources. In environmental science, bioinformatics is used to study the impact of human activities on ecosystems, identify new sources of renewable energy, and monitor the health of the planet. In forensics, bioinformatics is used to analyze DNA evidence and identify individuals involved in criminal activities.Despite the many benefits of bioinformatics, there are also significant challenges and ethical considerations that need to be addressed. As the amount of biological data continues to grow, there is an increasing need for efficient data storage, management, andsecurity systems. Additionally, the interpretation of biological data requires a deep understanding of both biological and computational principles, which can be a barrier for some researchers and healthcare providers.Furthermore, the use of bioinformatics in areas such as personalized medicine and forensics raises important ethical questions regarding privacy, informed consent, and the potential for discrimination based on genetic information. It is crucial that the development and application of bioinformatics technologies be guided by strong ethical principles and robust regulatory frameworks to ensure that they are used in a responsible and equitable manner.In conclusion, bioinformatics is a rapidly evolving field that is transforming the way we understand and interact with the biological world. By combining the power of computer science and information technology with the insights of biology, bioinformatics is enabling new discoveries, improving human health, and shaping the future of scientific research. As the field continues to grow and evolve, it will be important for researchers, policymakers, and the public to work together to ensure that the benefits of bioinformatics are realized in a responsible and ethical manner.。
生物信息学复习题已附答案
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生物信息学复习题一、填空题1、识别基因主要有两个途径即基因组DNA外显子识别和基于EST策略的基因鉴定。
2、表达序列标签是从mRNA 中生成的一些很短的序列（300-500bp），它们代表在特定组织或发育阶段表达的基因。
3、序列比对的基本思想，是找出检测基因和目标序列的相似性，就是通过在序列中插入空位的方法使所比较的序列长度达到一致。
比对的数学模型大体分为两类，分别是整体比对和局部比对。
4、2-DE的基本原理是根据蛋白质等电点和分子量不同，进行两次电泳将之分离。
第一向是等电聚焦分离,第二向是SDS-PAGE分离。
5、蛋白质组研究的三大关键核心技术是双向凝胶电泳技术、质谱鉴定技术、计算机图像数据处理与蛋白质数据库。
二、判断题1、生物体的结构和功能越复杂的种类就越多，所需要的基因也越多，C值越大，这是真核生物基因组的特点之一。
（对）2、CDS一定就是ORF。
（对）3、两者之间有没有共同的祖先，可以通过序列的同源性来确定，如果两个基因或蛋白质有着几乎一样的序列，那么它们高度同源,就具有共同的祖先。
（错）4、STS，是一段200-300bp的特定DNA序列，它的序列已知，并且在基因组中属于单拷贝。
（对）5、非编码DNA是“垃圾DNA”，不具有任何的分析价值，对于细胞没有多大的作用。
（错）6、基因树和物种树同属于系统树，它们之间可以等同。
（错）7、基因的编码序列在DNA分子上是被不编码的序列隔开而不连续排列的。
( 对）8、对任意一个DNA序列，在不知道哪一个碱基代表CDS的起始时，可用6框翻译法，获得6个潜在的蛋白质序列。
（对）9、一个机体只有一个确定的基因组，但基因组内各个基因表达的条件和表达的程度随时间、空间和环境条件而不同。
（对）10、外显子和内含子之间没有绝对的区分，一个基因的内含子可以是另一个基因的外显子，同一个基因在不同的生理状况或生长发育的不同阶段，外显子组成也可以不同。