2009-11-05 21:28:08| 分类：
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.
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
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
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.
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
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.
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.
A neural network in which input and output states are directly connected without intervening hidden layers.
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.
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.
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.
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）
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)
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.
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）
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.
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.
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
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.)
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.
Q20 (Quality score 20)
quality score of > or = 20 indicates that there is less than a 1 in
100 chance that the base call is incorrect. These are consequently
high-quality bases. Specifically, the quality value "q" assigned to a basecall is defined as:
q = -10 x log10(p)
where p is the estimated error probability for that basecall. Note that high quality values correspond to low error probabilities, and conversely.
is an algorithm which uses a sliding window of 50 bases and trims from
the 5' end of the read followed by the 3' end. With each window, the
number of low quality (10 or less) bases is determined. If more than 5
bases are below the threshold quality, the window is incremented by one
base and the process is repeated. When the low quality test fails, the
position where it stopped is recorded. The parameters for window length
low quality threshold and number of low quality bases tolerated are
fixed. The positions of the 5' and 3' boundaries of the quality region
are noted in the plot of quality values presented in the" Chromatogram Details" report.
The input sequence (or other type of search term) with which all of the entries in a database are to be compared.
Radiation hybrid (RH) map （辐射杂交图谱）
genome map in which STSs are positioned relative to one another on the
basis of the frequency with which they are separated by
radiation-induced breaks. The frequency is assayed by analysing a panel
of human–hamster hybrid cell lines, each produced by lethally
irradiating human cells and fusing them with recipient hamster cells
such that each carries a collection of human chromosomal fragments. The
unit of distance is centirays (cR), denoting a 1% chance of a break
occuring between two loci
Raw Score （初值，指最初得到的联配值S）
The score of
an alignment, S, calculated as the sum of substitution and gap scores.
Substitution scores are given by a look-up table (see PAM, BLOSUM). Gap
scores are typically calculated as the sum of G, the gap opening
penaltyand L, the gap extension penalty. For a gap of length n, the gap
cost would be G+Ln. The choice of gap costs, G and L is empirical, but
it is customary to choose a high value for G (10-15)and a low value for L (1-2).
Raw sequence （原始序列/读胶序列）
Individual unassembled sequence reads, produced by sequencing of clones containing DNA inserts.
Receiver operator characteristic
receiver operator characteristic (ROC) curve describes the probability
that a test will correctly declare the condition present against the
probability that the test will declare the condition present when
actually absent. This is shown through a graph of the tesls sensitivity
against one minus the test specificity for different possible threshold
The presence of more
than one identical item represents redundancy. In bioinformatics, the
term is used with reference to the sequences in a sequence database. If
a database is described as being redundant, more than one identical
(redundant) sequence may be found. If the database is said to be
non-redundant (nr), the database managers have attempted to reduce the
redundancy. The term is ambiguous with reference to genetics, and as
such, the degree of non-redundancy varies according to the database
manager's interpretation of the term. One can argue whether or not two
alleles of a locus defines the limit of redundancy, or whether the same
locus in different, closely related organisms constitutes redundency.
Non-redundant databases are, in some ways, superior, but are less
complete. These factors should be taken into consideration when
selecting a database to search.
computational tool provides a method for expressing the variations
found in a set of related sequences including a range of choices at one
position, insertions, repeats, and so on. For example, these
expressions are used to characterize variations found in protein
domains in the PROSITE catalog.
A set of techniques for reducing data overfitting when training a model. See also Overfitting.
information into tables where each column represents the fields of
informa-tion that can be stored in a single record. Each row in the
table corresponds to a single record. A single database can have many
tables and a query language is used to access the data. See also
The result of
connecting contigs by linking information from paired-end reads from
plasmids, paired-end reads from BACs, known messenger RNAs or other
sources. The contigs in a scaffold are ordered and oriented with
respect to one another.
See Position-specific scoring matrix.
program for filtering low complexity regions in amino acid sequences.
Residues that have been masked are represented as "X" in an alignment.
SEG filtering is performed by default in the blastp subroutine of BLAST
2.0. (Wootton and Federhen)
Selectivity (in database similarity searches)（数据库相似性搜索的选择准确性）
ability of a search method to locate members of a protein family
without making a false-positive classification of members of other
Sensitivity (in database similarity searches)（数据库相似性搜索的灵敏性）
ability of a search method to locate as many members of a protein
family as possi-ble, including distant members of limited sequence
Sequence Tagged Site （序列标签位点）
Short cDNA sequences of
regions that have been physically mapped. STSs provide unique
landmarks, or identifiers, throughout the genome. Useful as a framework
for further sequencing.
A significant result
is one that has not simply occurred by chance, and therefore is
prob-ably true. Significance levels show how likely a result is due to
chance, expressed as a probability. In sequence analysis, the
significance of an alignment score may be calcu-lated as the chance
that such a score would be found between random or unrelated sequences.
See Expect value.
Similarity score (sequence alignment) （相似性值）
means the extent to which nucleotide or protein sequences are related.
The extent of similarity between two sequences can be based on percent
sequence identity and/or conservation. In BLAST similarity refers to a
positive matrix score. The sum of the number of identical matches and
conservative (high scoring) substitu-tions in a sequence alignment
divided by the total number of aligned sequence charac-ters. Gaps are
A search algorithm that
attempts to solve the problem of finding global extrema. The algorithm
was inspired by the physical cooling process of metals and the freezing
process in liquids where atoms slow down in movement and line up to
form a crystal. The algorithm traverses the energy levels of a
function, always accepting energy levels that are smaller than previous
ones, but sometimes accepting energy levels that are greater, according
to the Boltzmann probability distribution.
Single-linkage cluster analysis
analysis of a group of related objects, e.g., similar proteins in
different genomes to identify both close and more distantrelationships,
represented on a tree or dendogram. The method joins the most closely
related pairs by the neighbor-joining algorithm by representing these
pairs as outer branches onthe tree. More distant objects are then
pro-gressively added to lower tree branches. The method is also used to
predict phylogenet-ic relationships by distance methods. See also
Hierarchical clustering, Neighbor-joining method.
dynamic programming to find local alignments between sequences. The key
fea-ture is that all negative scores calculated in the dynamic
programming matrix are changed to zero in order to avoid extending
poorly scoring alignments and to assist in identifying local alignments
starting and stopping anywhere with the matrix.
nucleotide polymorphism, or a single nucleotide position in the genome
sequence for which two or more alternative alleles are present at
appreciable frequency (traditionally, at least 1%) in the human
Space or time complexity（时间或空间复杂性）
complexity is the maximum amount of computer memory or time required
for the number of algorithmic steps to solve a problem.
Specificity (in database similarity searches)（数据库相似性搜索的特异性）
The ability of a search method to locate members of one protein family, including dis-tantly related members.
sequence repeat, a sequence consisting largely of a tandem repeat of a
specific k-mer (such as (CA)15). Many SSRs are polymorphic and have
been widely used in genetic mapping.
Stochastic context-free grammar
formal representation of groups of symbols in different parts of a
sequence; i.e., not in the same context. An example is complementary
regions in RNA that will form sec-ondary
structures. The stochastic feature introduces variability into such regions.
Refers to the minimum number of matches required within a window. See also Filtering.
See Sequence Tagged Site
presence of a non-identical amino acid at a given position in an
alignment. If the aligned residues have similar physico-chemical
properties the substitution is said to be "conservative".
Substitution Matrix （替换矩阵）
A substitution matrix containing values
proportional to the probability that amino acid i mutates into amino
acid j for all pairs of amino acids. such matrices are constructed by
assembling a large and diverse sample of verified pairwise alignments
of amino acids. If the sample is large enough to be statistically
significant, the resulting matrices should reflect the true
probabilities of mutations occuring through a period of evolution.Sum
of pairs method
Sums the substitution scores of all possible
pair-wise combinations of sequence charac-ters in one column of a
multiple sequence alignment.
A non-redundant (See Redundancy) protein sequence database. Thoroughly annotated and cross referenced. A subdivision is TrEMBL.
The presence of a set of homologous genes in the same order on two genomes.
protein structure prediction, the aligning of the sequence of a protein
of unknown structure with a known three-dimensional structure to
determine whether the amino acid sequence is spatially and chemically
compatible with that structure.
A protein sequence database of Translated EMBL nucleotide sequences.
information theory, a logarithmic measure of the average number of
choices that must be made for identification purposes. See also
Unified Modeling Language (UML)
A standard sanctioned by the Object Management Group that provides a formal nota-tion for describing object-oriented design.
of unique human genes, at NCBI. Entries are selected by near identical
presence in GenBank and dbEST databases. The clusters of sequences
produced are considered to represent a single gene.
Unitary Matrix （一元矩阵）
Also known as Identity Matrix. A scoring system in which only identical characters receive a positive score.
Uniform resource locator.
Calculates the optimal path of a sequence through a hidden Markov model of sequences using a dynamic programming algorithm.
See Position-specific scoring matrix.