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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

附录:生物信息学主要英文术语及释义

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, any significant

matches 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.

ASCII

The 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 underlying

distribution 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 units

From 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 the similarity 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 analysis

A 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 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)

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.

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 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 usage

Analysis 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 grammars

A 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.

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)

See coverage

Dirichlet mixtures

Defined 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 and possessing 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: https://www.wendangku.net/doc/078083310.html,/ 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 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)

See Expressed Sequence Tag

Expect 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 and Lipman)

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 analysis

Studies 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 algorithm

Used 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 method

An 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 two or

more 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-bits

Some 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 that particular 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 between

states 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 climbing

A 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

HTML(超文本标识语言)

The Hyper-Text Markup Language (HTML) provides a structural description of a document using a specified tag set. HTML currently serves as the Internet lingua franca for describing hypertext Web page documents.

Hyperplane

A generalization of the two-dimensional plane to N dimensions.

Hypercube

A generalization of the three-dimensional cube to N dimensions.

Identity (相同性/相同率)

The extent to which two (nucleotide or amino acid) sequences are invariant. Indel(插入或删除的缩略语)

An insertion or deletion in a sequence alignment.

Information content (of a scoring matrix)

A representation of the degree of sequence conservation in a column of a

scoring matrix representing an alignment of related sequences. It is also the number of questions that must be asked to match the column to a position in a test sequence. For bases, the max-imum possible number is 2, and for proteins, 4.32 (logarithm to the base 2 of the number of possible sequence characters).

Information theory(信息理论)

A branch of mathematics that measures information in terms of bits, the minimal amount of structural complexity needed to encode a given piece of information.

Input layer(输入层)

The initial layer in a feed-forward neural net. This layer encodes input information that will be fed through the network model.

Interface definition language

Used to define an interface to an object model in a programming language neutral form, where an interface is an abstraction of a service defined only by the operations that can be performed on it.

Internet(因特网)

The network infrastructure, consisting of cables interconnected by routers, that pro-vides global connectivity for individual computers and private networks of computers. A second sense of the word internet is the collective computer resources available over this global network.

Interpolated Markov model

A type of Markov model of sequences that examines sequences for patterns of variable length in order to discriminate best between genes and non-gene sequences.

Intranet(内部网)

Intron (内含子)

Non-coding region of DNA.

Iterative(反复的/迭代的)

A sequence of operations in a procedure that is performed repeatedly.

Java(一种由SUN Microsystem开发的编程语言)

K (BLAST程序的一个统计参数)

A statistical parameter used in calculating BLAST scores that can be thought of as a natural scale for search space size. The value K is used in converting a raw score (S) to a bit score (S').

K-tuple(字/字长)

Identical short stretches of sequences, also called words.

lambda (λ,BLAST程序的一个统计参数)

A statistical parameter used in calculating BLAST scores that can be thought of as a natural scale for scoring system. The value lambda is used in converting a raw score (S) to a bit score (S').

LAN(局域网)

Local area network.

Likelihood(似然性)

The hypothetical probability that an event which has already occurred would yield a specific outcome. Unlike probability, which refers to future events, likelihood refers to past events.

Linear discriminant analysis

An analysis in which a straight line is located on a graph between two sets of data pointsin a location that best separates the data points into two groups. Local alignment(局部联配)

Attempts to align regions of sequences with the highest density of matches. In doing so, one or more islands of subalignments are created in the aligned sequences.

Log odds score(概率对数值)

The logarithm of an odds score. See also Odds score.

Low Complexity Region (LCR) (低复杂性区段)

Regions of biased composition including homopolymeric runs, short-period repeats, and more subtle overrepresentation of one or a few residues. The SEG program is used to mask or filter LCRs in amino acid queries. The DUST program is used to mask or filter LCRs in nucleic acid queries.

Machine learning(机器学习)

The training of a computational model of a process or classification scheme to distinguish between alternative possibilities.

Markov chain(马尔可夫链)

Describes a process that can be in one of a number of states at any given time. The Markov chain is defined by probabilities for each transition occurring; that is, probabilities of the occurrence of state sj given that the current state is sp Substitutions in nucleic acid and protein sequences are generally assumed to follow a Markov chain in that each site changes independently of the previous history of the site. With this model, the number and types of substitutions observed over a relatively short period of evolutionary time can be extrapolated to longer periods of time. In performing sequence alignments and calculating the statistical significance of alignment scores, sequences are assumed to be Markov chains in which the choice of one sequence position is not influenced by another.

Masking (过滤)

Also known as Filtering. The removal of repeated or low complexity regions from a sequence in order to improve the sensitivity of sequence similarity searches performed with that sequence.

Maximum likelihood (phylogeny, alignment)(最大似然法)

The most likely outcome (tree or alignment), given a probabilistic model of evolutionary change in DNA sequences.

Maximum parsimony(最大简约法)

The minimum number of evolutionary steps required to generate the observed variation in a set of sequences, as found by comparison of the number of steps in all possible phylogenetic trees.

Method of moments

The mean or expected value of a variable is the first moment of the values of the variable around the mean, defined as that number from which the sum of deviations to all values is zero. The standard deviation is the second moment of the values about the mean, and so on.

Minimum spanning tree

Given a set of related objects classified by some similarity or difference score, the mini-mum spanning tree joins the most-alike objects on adjacent outer branches of a tree and then sequentially joins less-alike objects by more inward branches. The tree branch lengths are calculated by the same neighbor-joining algorithm that is used to build phylogenetic trees of sequences from a distance matrix. The sum of the resulting branch lengths between each pair of objects will be approximately that found by the classification scheme.

MMDB (分子建模数据库)

Molecular Modelling Database. A taxonomy assigned database of PDB (see PDB) files, and related information.

Molecular clock hypothesis(分子钟假设)

The hypothesis that sequences change at the same rate in the branches of an evolutionary

tree.

Monte Carlo(蒙特卡罗法)

A method that samples possible solutions to a complex problem as a way to estimate a more general solution.

Motif (模序)

A short conserved region in a protein sequence. Motifs are frequently highly conserved parts of domains.

Multiple Sequence Alignment (多序列联配)

An alignment of three or more sequences with gaps inserted in the sequences such that residues with common structural positions and/or ancestral residues are aligned in the same column. Clustal W is one of the most widely used multiple sequence alignment programs

Mutation data matrix(突变数据矩阵,即PAM矩阵)

A scoring matrix compiled from the observation of point mutations between aligned sequences. Also refers to a Dayhoff PAM matrix in which the scores are given as log odds scores.

N50 length (N50长度,即覆盖50%所有核苷酸的最大序列重叠群长度)

A measure of the contig length (or scaffold length) containing a 'typical' nucleotide. Specifically, it is the maximum length L such that 50% of all nucleotides lie in contigs (or scaffolds) of size at least L.

Nats (natural logarithm)

A number expressed in units of the natural logarithm.

NCBI (美国国家生物技术信息中心)

National Center for Biotechnology Information (USA). Created by the United States Congress in 1988, to develop information systems to support the

biological research community.

Needleman-Wunsch algorithm(Needleman-Wunsch算法)

Uses dynamic programming to find global alignments between sequences. Neighbor-joining method(邻接法)

Clusters together alike pairs within a group of related objects (e.g., genes with similar sequences) to create a tree whose branches reflect the degrees of difference among the objects.

Neural network(神经网络)

From artificial intelligence algorithms, techniques that involve a set of many simple units that hold symbolic data, which are interconnected by a network of links associated with numeric weights. Units operate only on their symbolic data and on the inputs that they receive through their connections. Most neural networks use a training algorithm (see Back-propagation) to adjust connection weights, allowing the network to learn associations between various input and output patterns. See also Feed-forward neural network.

NIH (美国国家卫生研究院)

National Institutes of Health (USA).

Noise(噪音)

In sequence analysis, a small amount of randomly generated variation in sequences that is added to a model of the sequences; e.g., a hidden Markov model or scoring matrix, in order to avoid the model overfitting the sequences. See also Overfitting.

Normal distribution(正态分布)

The distribution found for many types of data such as body weight, size, and exam scores. The distribution is a bell-shaped curve that is described by a mean and standard deviation of the mean. Local sequence alignment scores between unrelated or random sequences do not follow this distribution but instead the extreme value distribution which has a much extended tail for higher scores. See also Extreme value distribution.

Object Management Group (OMG)(国际对象管理协作组)

A not-for-profit corporation that was formed to promote component-based software by introducing standardized object software. The OMG establishes industry guidelines and detailed object management specifications in order to provide a common framework for application development. Within OMG is a Life Sciences Research group, a consortium representing pharmaceutical companies, academic institutions, software vendors, and hardware vendors who are working together to improve communication and inter-operability among computational resources in life sciences research. See CORBA. Object-oriented database(面向对象数据库)

Unlike relational databases (see entry), which use a tabular structure, object-oriented databases attempt to model the structure of a given data set as closely as possible. In doing so, object-oriented databases tend to reduce the appearance of duplicated data and the complexity of query structure often found in relational databases.

Odds score(概率/几率值)

The ratio of the likelihoods of two events or outcomes. In sequence alignments and scoring matrices, the odds score for matching two sequence characters is the ratio of the frequency with which the characters are aligned in related sequences divided by the frequency with which those same two characters align by chance alone, given the frequency of occurrence of each in the sequences. Odds scores for a set of individually aligned positions are obtained by multiplying the odds scores for each position. Odds scores are often converted to logarithms to create log odds scores that can be added to obtain the log odds score of a sequence alignment.

OMIM (一种人类遗传疾病数据库)

Online Mendelian Inheritance in Man. Database of genetic diseases with references to molecular medicine, cell biology, biochemistry and clinical details of the diseases.

Optimal alignment(最佳联配)

The highest-scoring alignment found by an algorithm capable of producing multiple solutions. This is the best possible alignment that can be found, given any parameters supplied by the user to the sequence alignment program.

ORF (开放阅读框)

Open Reading Frame. A series of codons (base triplets) which can be translated into a protein. There are six potential reading frames of an unidentifed sequence; TBLASTN (see BLAST) transalates a nucleotide sequence in all six reading frames, into a protein, then attempts to align the results to sequeneces in a protein database, returning the results as a nucleotide sequence. The most likely reading frame can be identified using on-line software (e.g. ORF Finder).

Orthologous(直系同源)

Homologous sequences in different species that arose from a common ancestral gene during speciation; may or may not be responsible for a similar function. A pair of genes found in two species are orthologous when the encoded proteins are 60-80% identical in an alignment. The proteins almost certainly have the same three-dimensional structure, domain structure, and biological function, and the encoding genes have originated from a common ancestor gene at an earlier evolutionary time. Two orthologs 1 and II in genomes A and B, respectively, may be identified when the complete genomes of two species are available: (1) in a database similarity search of all of the proteome of B using I as a query, II is the best hit found, and (2) I is the best hit when 11 is used as a query of the proteome of B. The best hit is the database sequence with the highest expect value (E). Orthology is also predicted by a very close phylogenetic relationship between sequences or by a cluster analysis. Compare to Paralogs. See also Cluster analysis.

Output layer(输出层)

The final layer of a neural network in which signals from lower levels in the network are input into output states where they are weighted and summed to

give an outpu t signal. For example, the output signal might be the prediction of one type of protein secondary structure for the central amino acid in a sequence window.

Overfitting

Can occur when using a learning algorithm to train a model such as a neural net or hid-den Markov model. Overfitting refers to the model becoming too highly representative of the training data and thus no longer representative of the overall range of data that is supposed to be modeled.

P value (P值/概率值)

The probability of an alignment occurring with the score in question or better. The p value is calculated by relating the observed alignment score, S, to the expected distribution of HSP scores from comparisons of random sequences of the same length and composition as the query to the database. The most highly significant P values will be those close to 0. P values and E values are different ways of representing the significance of the alignment.

Pair-wise sequence alignment(双序列联配)

An alignment performed between two sequences.

PAM (可接受突变百分率/可以观察到的突变百分率,它可作为一种进化时间单位)

Percent Accepted Mutation. A unit introduced by Dayhoff et al. to quantify the amount of evolutionary change in a protein sequence. 1.0 PAM unit, is the amount of evolution which will change, on average, 1% of amino acids in a protein sequence. A PAM(x) substitution matrix is a look-up table in which scores for each amino acid substitution have been calculated based on the frequency of that substitution in closely related proteins that have experienced a certain amount (x) of evolutionary divergence.

Paralogous (旁系同源)

Homologous sequences within a single species that arose by gene duplication. Genes that are related through gene duplication events. These events may lead to the production of a family of related proteins with similar biological functions within a species. Paralogous gene families within a species are identified by using an individual protein as a query in a database similarity search of the entireproteome of an organism. The process is repeated for the entire proteome and the resulting sets of related proteins are then searched for clusters that are most likely to have a conserved domain structure and should represent a paralogous gene family.

Parametric sequence alignment

An algorithm that finds a range of possible alignments based on varying the parameters of the scoring system for matches, mismatches, and gap penalties. An example is the Bayes block aligner.

PDB (主要蛋白质结构数据库之一)

Brookhaven Protein Data Bank. A database and format of files which describe the 3D structure of a protein or nucleic acid, as determined by X-ray crystallography or nuclear magnetic resonance (NMR) imaging. The

molecules described by the files are usually viewed locally by dedicated software, but can sometimes be visualised on the world wide web.

Pearson correlation coefficent(Pearson相关系数)

A measure of the correlation between two variables that reflects the degree to which the two variables are related. For example, the coefficient is used as a measure of similarity of gene expression in a microarray experiment. See also Correlation coefficient. Percent identity The percentage of the columns in an alignment of two sequences that includes identical amino acids. Columns in the alignment that include gaps are not scored in the calculation.

Percent similarity(相似百分率)

The percentage of the columns in an alignment of two sequences that includes either identical amino acids or amino acids that are frequently found substituted for each other in sequences of related proteins (conservative substitutions). These substitutions may be found in an amino acid substitution matrix such as the Dayhoff PAM and Henikoff BLOSUM matrices. Columns in the alignment that include gaps are not scored in the calculation.

Perceptron(感知器,模拟人类视神经控制系统的图形识别机)

A neural network in which input and output states are directly connected without intervening hidden layers.

PHRED (一种广泛应用的原始序列分析程序,可以对序列的各个碱基进行识别和质量评价)

A widely used computer program that analyses raw sequence to produce a 'base call' with an associated 'quality score' for each position in the sequence.

A PHRED quality score of X corresponds to an error probability of approximately 10-X/10. Thus, a PHRED quality score of 30 corresponds to 99.9% accuracy for the base call in the raw read.

PHRAP (一种广泛应用的原始序列组装程序)

A widely used computer program that assembles raw sequence into sequence contigs and assigns to each position in the sequence an associated 'quality score', on the basis of the PHRED scores of the raw sequence reads. A PHRAP quality score of X corresponds to an error probability of approximately 10-X/10. Thus, a PHRAP quality score of 30 corresponds to 99.9% accuracy for a base in the assembled sequence.

Phylogenetic studies(系统发育研究)

PIR (主要蛋白质序列数据库之一,翻译自GenBank)

A database of translated GenBank nucleotide sequences. PIR is a redundant (see Redundancy) protein sequence database. The database is divided into four categories:

PIR1 - Classified and annotated.

PIR2 - Annotated.

PIR3 - Unverified.

PIR4 - Unencoded or untranslated.

Poisson distribution(帕松分布)

Used to predict the occurrence of infrequent events over a long period of time

or when there are a large number of trials. In sequence analysis, it is used to calculate the chance that one pair of a large number of pairs of unrelated sequences may give a high local alignment score.

Position-specific scoring matrix (PSSM)(特定位点记分矩阵,PSI-BLAST 等搜索程序使用)

The PSSM gives the log-odds score for finding a particular matching amino acid in a target sequence. Represents the variation found in the columns of an alignment of a set of related sequences. Each subsequent matrix column corresponds to the next column in the alignment and each row corresponds to a particular sequence character (one of four bases in DNA sequences or 20 amino acids in protein sequences). Matrix values are log odds scores obtained by dividing the counts of the residue in the alignment, dividing by the expected number of counts based on sequence composition, and converting the ratio to a log score. The matrix is moved along sequences to find similar regions by adding the matching log odds scores and looking for high values. There is no allowance for gaps. Also called a weight matrix or scoring matrix. Posterior (Bayesian analysis)

A conditional probability based on prior knowledge and newly evaluated relationships among variables using Bayes rule. See also Bayes rule.

Prior (Bayesian analysis)

The expected distribution of a variable based on previous data.

Profile(分布型)

A matrix representation of a conserved region in a multiple sequence alignment that allows for gaps in the alignment. The rows include scores for matching sequential columns of the alignment to a test sequence. The columns include substitution scores for amino acids and gap penalties. See also PSSM.

Profile hidden Markov model(分布型隐马尔可夫模型)

A hidden Markov model of a conserved region in a multiple sequence alignment that includes gaps and may be used to search new sequences for similarity to the aligned sequences.

Proteome(蛋白质组)

The entire collection of proteins that are encoded by the genome of an organism. Initially the proteome is estimated by gene prediction and annotation methods but eventually will be revised as more information on the sequence of the expressed genes is obtained.

Proteomics (蛋白质组学)

Systematic analysis of protein expression of normal and diseased tissues that involves the separation, identification and characterization of all of the proteins in an organism.

Pseudocounts

Small number of counts that is added to the columns of a scoring matrix to increase the variability either to avoid zero counts or to add more variation than was found in the sequences used to produce the matrix.

附录1常用基本词汇表

附录1 常用基本词汇表 英文名词中文名词解释 A(Adenine)腺嘌呤作为碱基的两种嘌呤中的一种。 active site活化位点蛋白质三维表面催化作用发生的区域。 alignment比对为了确定两个同源核酸或蛋白质序列的累计差 异而进行的配对称为比对。 alignment of alignments比对的比对即比对的对象不是简单的序列,而是序列的比 对。 alleles等位基因一个基因的不同版本。 alpha carbonα碳在氨基酸中与侧链(R-基团)相连的中心碳原子。 alternative splicing可变剪接从一个单独的hnRNA生成两个或多个mRNA 分子的过程。 amino terminus (N-terminal)氨基端(N端)在一个多肽中,具有自由氨基的分子端,对应 于基因的5’-端。 anti-parallel反向平行表示相反的方向;在双链DNA中,这意味着如果 一条链是5' 到3'的,则其互补链方向是3' 到 5'的。 backbone (of an amino acid) (氨基酸的)骨架包含一个氨基,一个α碳和一个羧酸或羧基。base pair 碱基对(1)在双链DNA中嘌呤和嘧啶之间的相互作用 (特别指A和T之间,G和C之间);(2)双链 DNA序列长度的基本单位。 beta turnsβ转角在反向平行的β折叠片中,当β链反转方向的时 候蛋白质内部形成的U型结构。 Bioinformatics 生物信息学应用信息科学的理论、方法和技术,管理、分析 和利用生物分子数据。 Biocomputing生物计算本书中特指用计算机技术分析和处理生物分子 数据。

国际贸易术语中英文

外销员辅导物流货运费英文术语大全 海运费 ocean freight 集卡运费、短驳费 Drayage 订舱费 booking charge 报关费 customs clearance fee 操作劳务费 labour fee or handling charge 商检换单费 exchange fee for CIP 换单费 D/O fee 拆箱费 De-vanning charge 港杂费 port sur-charge 电放费 B/L surrender fee 冲关费 emergent declearation change 海关查验费 customs inspection fee 待时费 waiting charge 仓储费 storage fee 改单费 amendment charge 拼箱服务费 LCL service charge 动、植检疫费 animal & plant quarantine fee 移动式其重机费 mobile crane charge 进出库费 warehouse in/out charge 提箱费 container stuffing charge 滞期费 demurrage charge 滞箱费 container detention charge 卡车运费 cartage fee 商检费 commodity inspection fee 转运费 transportation charge 污箱费 container dirtyness change 坏箱费用 container damage charge 清洁箱费 container clearance charge 分拨费 dispatch charge 车上交货 FOT ( free on track ) 电汇手续费 T/T fee 转境费/过境费 I/E bonded charge 空运方面的专用术语 空运费 air freight 机场费 air terminal charge 空运提单费 airway bill fee FSC (燃油附加费) fuel surcharge SCC(安全附加费) security sur-charge 抽单费 D/O fee 上海港常用术语 内装箱费 container loading charge(including inland drayage) 疏港费 port congestion charge 他港常用术语

国际贸易实务英文名词解释(英to英)

国际贸易实务英文名词解释(英to英) What’s International Trade? The international trade is the exchange of goods and services produced in one country for goods and services produced in another country. EXPORTING Exporting is the process of earning money by providing the right product at the right price at the right time in the right place beyond your home boundary. The ultimate goal is to make sure that the exporter is to be paid for the goods he sells. EXW EXW means the seller delivers when he places the goods at the disposal of the buyer at the seller’s premises (法定地址) or another named place. The seller doesn’t not declare the goods for export and he needn’t load goods on any collecting vehicle. FAS Free alongside ship means that the seller delivers when the goods are placed alongside the vessel at named port of shipment. This means that the buyer has to bear all costs and risks of the goods from that moment. FOB Free on Board means the seller delivers when the goods pass the ship’s rail at the named port of shipment. This means that the buyer has to bear all the costs and risks from that point. The FOB terms require the seller to clear the goods for export. CFR Cost and freight means that the seller delivers when the goods pass ship’s rail at the named port of shipment CIF CIF means that the seller bears the same obligations as under CFR. In additional that he has to procure marine insurance against the buyer’s risk of loss or damage to the goods during the carriage. The seller contracts for insurance and pay the insurance premium. FCA, Free carrier (…Named place) It means that the seller fulfils his obligation to deliver when he has handed over the goods, cleared for export, into the custody of the carrier named by the buyer at the named place or point. If no precise point is indicated by the buyer, the seller may choose within the place or range stipulated where the carrier shall take charge of the goods. When, according to commercial practices, the seller’s assistance is required in making the contract with the carrie r, the seller may act at the buyer’s risk and expenses.

计算机英语常用词汇

计算机英语常用词汇(计算机科学版)2009-04-18 10:16:24 分类: (一个进程的)激活activation(of a procedure) 活动服务器界面Active Server Pages,ASP 角色Actors 实参actual parameter Ada(一种基于pascal的程序设计语言) 自适应词典编码adaptive dictionary encoding 适配器模式adaptor pattern (存储单元的)地址address(of memory cell) 地址多项式address polynomial Adleman,Leonard 管理员administrator Adobe系统Adobe Systems 代理agent Alexander,Christopher 代数编码理论Algebraic coding theory 算法algorithm 算法的发现discovery of 算法的有效性/正确性complexity / efficiency of 算法的表示representation of 算法的检验verification of 算法分析algorithm analysis 反网络域名抢注消费者保护法案the Anticybersquatting Consumer Protection Act 防病毒软件antivirus software APL A Programming Language的缩写,是用于远程终端的一种程序语言 苹果计算机公司Apple Computer,Inc. Applet(Java程序) 应用层(因特网)application layer 应用编程接口(API)Application Programmer Interface 应用软件Application software 谓词的变元argument(of a predicate) 亚里斯多德(Aristotle) 移位Arithmetic shift 数组Array 异构数组heterogeneous 同构数组homogeneous 人工智能Artificial intelligence 人工神经网络Artificial neural network ASCII.参见美国信息交换标准码 Asimo机器人 ASP见活动服务器界面 汇编程序Assembler 汇编语言Assembly language

国际贸易术语英文缩写

国际贸易术语英文缩写

国际贸易术语英文缩写 A AA制自动许可制 AAC 亚非会议 A.A.R 保综合险(一切险) ABCコ-ド ABC商业密码ac. 英亩 a/c(或A/C) 银行往来存款acpt 承兑;接受 a/cs pay. 应付帐款 a/cs rec. 应收帐款ACU 亚洲清算同盟 A/D 出票后 ADB 亚洲开发银行a.f. 预付运费 AFA 自动外汇分配制度AFDB 非洲开发银行 A.F.E. B. 核准的外汇银行agcy 代理公司 agt. 代理人 AIQ制自动进口配额制A.M. 互相保险

A.N. 到货通知 A/P 委托付款证 A/P 委托购买证 A/P 附加保险费 A/P 付讫 APO 亚洲生产率组织 APU 亚洲支付同盟 A/R 综合险,一切险 A/S 销货帐单 A/S 见票后 A/S 见票即付 ASEAN 东南亚国家联盟 ASP 美国销售价格 ATAカルネ暂时许可簿册,临时过境证A.T.L. 实际全损 A/V 从价 A/W 实际重量 A.W. B. 空运单 B B/Aレ-ト银行承兑利率 B/B 买入汇票 B/C 托收汇票

B/D 银行贴现 B/D 银行汇票 B/E 入港申报单 B/E 汇票 BETRO 英国出口贸易研究组织BIS 国际清算银行 B/G 保税货物 B/L 提单 B/N 钞票 B/N 交货记录 B.O. 分公司 B.P. 应付票据 B.R. 应收票据 B/S 再进口免税证 B/St 即票 BTN 布鲁塞尔税则分类 B.T.T. 银行电汇 C C.A. D. 凭单付款

C.B. D. 交货前付款 C.B.S. 装船前预付货款 C/C 商会 C.C. 时价 CCC 关税合作理事会 CCCN 关税合作理事会税则分类表 C.F.S. 集装箱货运站 C.H. 货舱 C.H. 票据交换所 C.H. 海关 Chq. 支票 C.I. 领事签证发票 C/I 保险证书 CIF関税込条件成本,保险费,运费加关税条件 CIF条件成本,保险加运费条件 CIF通関費用込条件成本,保险费,运费和一切进口费用条件 CIF&C条件成本,保险费,运费加佣金条件 CIFに関する国際統一規則 CIF买卖契约统一规则

《国际贸易术语解释通则)

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