A structure-based method for protein sequence alignment | Zendy

Maricel G. Kann | Zendy; P. A. Thiessen | Zendy; Anna R. Panchenko | Zendy; A. A. Schaffer | Zendy; Stephen F. Altschul | Zendy; Stephen H. Bryant | Zendy

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A structure-based method for protein sequence alignment

Author(s) -

Maricel G. Kann,

P. A. Thiessen,

Anna R. Panchenko,

A. A. Schaffer,

Stephen F. Altschul,

Stephen H. Bryant

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/bti233

Subject(s) - multiple sequence alignment , computer science , sequence alignment , domain (mathematical analysis) , sequence (biology) , protein domain , protein sequencing , conserved sequence , computational biology , data mining , protein structure , structural alignment , peptide sequence , biology , genetics , mathematics , mathematical analysis , biochemistry , gene

With the continuing rapid growth of protein sequence data, protein sequence comparison methods have become the most widely used tools of bioinformatics. Among these methods are those that use position-specific scoring matrices (PSSMs) to describe protein families. PSSMs can capture information about conserved patterns within families, which can be used to increase the sensitivity of searches for related sequences. Certain types of structural information, however, are not generally captured by PSSM search methods. Here we introduce a program, Structure-based ALignment TOol (SALTO), that aligns protein query sequences to PSSMs using rules for placing and scoring gaps that are consistent with the conserved regions of domain alignments from NCBI's Conserved Domain Database.

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