Bioinformatics Glossary


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. Themolecules 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 timeor 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.

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.

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.

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.PSI-BLAST (BLAST系列程序之一)
Position-Specific Iterative BLAST. An iterative search using the BLAST algorithm. A profile is built after the initial search, which is then used in subsequent searches. The process may be repeated, if desired with new sequences found in each cycle used to refine the profile. Details can be found in this discussion of PSI-BLAST. (Altschul et al.)

PSSM (特定位点记分矩阵)
See position-specific scoring matrix and profile.

Public sequence databases (公共序列数据库,指GenBank、EMBL和DDBJ)
The three coordinated international sequence databases: GenBank, the EMBL data library and DDBJ.

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