Comparative analysis of the quality of a global algorithm and a local algorithm for alignment of two sequences.

ABSTRACT:

Background

Algorithms of sequence alignment are the key instruments for computer-assisted studies of biopolymers. Obviously, it is important to take into account the "quality" of the obtained alignments, i.e. how closely the algorithms manage to restore the "gold standard" alignment (GS-alignment), which superimposes positions originating from the same position in the common ancestor of the compared sequences. As an approximation of the GS-alignment, a 3D-alignment is commonly used not quite reasonably. Among the currently used algorithms of a pair-wise alignment, the best quality is achieved by using the algorithm of optimal alignment based on affine penalties for deletions (the Smith-Waterman algorithm). Nevertheless, the expedience of using local or global versions of the algori

SUBMITTER: Polyanovsky VO 

PROVIDER: S-EPMC3223492 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature