Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs | Zendy

Ruslan I. Sadreyev | Zendy; Nick V. Grishin | Zendy

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Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs

Author(s) -

Ruslan I. Sadreyev,

Nick V. Grishin

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btg485

Subject(s) - diversity (politics) , similarity (geometry) , sequence (biology) , compass , quality (philosophy) , computer science , set (abstract data type) , sequence alignment , multiple sequence alignment , computational biology , biology , genetics , artificial intelligence , geography , peptide sequence , image (mathematics) , cartography , gene , physics , programming language , quantum mechanics , sociology , anthropology

Adding more distant homologs to a multiple alignment and thus increasing its diversity may eventually deteriorate the numerical profile constructed from this alignment. Here, we addressed the question whether such a diversity limit can be reached in the alignments of confident homologs found by PSI-BLAST, and we analyzed the dependence of the quality of the profile-profile comparison made by COMPASS on the sequence diversity within these alignments.

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