Therefore, sequence alignment is equivalent to searching for the SA intervals of substrings of X that match the query.
Note, that this representation [ 14] of an alignment is equivalent to an introduction of a gap symbol, as commonly used.
A simplified version of network alignment is equivalent to the maximum subgraph isomorphism problem, which is NP-complete, i.e. there is no efficient algorithm according to the computational complexity theory.
Though the lengths of the most abundant alignments were equivalent to the length of the query peptide, we observed some alignments as long as twice the length of the query peptide and such behavior was equally prevalent among hits to parental as well as to non-parental KO-families (Additional file 1: Figure S25).
A useful analogy may be a multiple sequence alignment: a sequence alignment aligns equivalent residues in different sequences and highlights regions with similar (conserved) residues, whereas the genome alignment in Figure 5 aligns equivalent genes in different genomes and highlights regions with similar (conserved) gene order.
An alignment of seven sequences was generated for each gene segment using the GTR model of nucleotide substitution, and the alignment length is equivalent to the length of the respective gene (e.g. the simulated alignment for HA is 1,778 bp in length).
"Expected" here means relative to the product of the frequencies of the amino acids in the individual columns of the alignment, which is equivalent to the assumption of no correlation between the two sites.
E-value (or expectation value or expect value) represents the number of different alignments with scores equivalent to or better than a given threshold S, that are expected to occur in a database search by chance.
Mathematically, finding the optimal alignment functions and is equivalent to minimizing the matching cost function defined as (25).
Simrank similarity scores are not equivalent to alignment percent similarities.
Given a pair of nucleotide sequences with one taken to be derived from the other, an alignment between them is equivalent to an accounting of the mutations via which the derivation occurred.
