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The process of lining up two or more sequences to achieve maximal levels of identity (and conservation, in the case of amino acid sequences) for the purpose of assessing the degree of similarity and the possibility of homology.

A fixed procedure embodied in a computer program.

The merger of biotechnology and information technology with the goal of revealing new insights and principles in biology.

Bit score
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.

Basic Local Alignment Search Tool. (Altschul et al.) A sequence comparison algorithm optimized for speed used to search sequence databases for optimal local alignments to a query. The initial search is done for a word of length "W" that scores at least "T" when compared to the query using a substitution matrix. Word hits are then extended in either direction in an attempt to generate an alignment with a score exceeding the threshold of "S". The "T" parameter dictates the speed and sensitivity of the search. For additional details, see one of the BLAST tutorials (Query or BLAST) or the narrative guide to BLAST.

Blocks Substitution Matrix. A substitution matrix in which scores for each position are derived from observations of the frequencies of substitutions in blocks of local alignments in related proteins. Each matrix is tailored to a particular evolutionary distance. In the BLOSUM62 matrix, for example, the alignment from which scores were derived was created using sequences sharing no more than 62% identity. Sequences more identical than 62% are represented by a single sequence in the alignment so as to avoid over-weighting closely related family members. (Henikoff and Henikoff)

Changes at a specific position of an amino acid or (less commonly, DNA) sequence that preserve the physico-chemical properties of the original residue.

A discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function.

A program for filtering low complexity regions from nucleic acid sequences.

E value
Expectation 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.

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)

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.

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.

Global Alignment
The alignment of two nucleic acid or protein sequences over their entire length.

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)

Similarity attributed to descent from a common ancestor.

High-scoring segment pair. Local alignments with no gaps that achieve one of the top alignment scores in a given search.

The extent to which two (nucleotide or amino acid) sequences are invariant.

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').

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').

Local Alignment
The alignment of some portion of two nucleic acid or protein sequences

Low Complexity Region (LCR)
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.

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.

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

Multiple Sequence Alignment
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

Optimal Alignment
An alignment of two sequences with the highest possible score.

Homologous sequences in different species that arose from a common ancestral gene during speciation; may or may not be responsible for a similar function.

P value
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.

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.

Homologous sequences within a single species that arose by gene duplication.

A table that lists the frequencies of each amino acid in each position of protein sequence. Frequencies are calculated from multiple alignments of sequences containing a domain of interest. See also PSSM.

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.

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.)

Position-specific scoring matrix; see profile. The PSSM gives the log-odds score for finding a particular matching amino acid in a target sequence.

The input sequence (or other type of search term) with which all of the entries in a database are to be compared.
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