Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage.

ABSTRACT:

Background

Development of sensitive sequence search procedures for the detection of distant relationships between proteins at superfamily/fold level is still a big challenge. The intermediate sequence search approach is the most frequently employed manner of identifying remote homologues effectively. In this study, examination of serine proteases of prolyl oligopeptidase, rhomboid and subtilisin protein families were carried out using plant serine proteases as queries from two genomes including A. thaliana and O. sativa and 13 other families of unrelated folds to identify the distant homologues which could not be obtained using PSI-BLAST.

Methodology/principal findings

We have proposed to start with multiple queries of classical serine protease members to identify remote hom

SUBMITTER: Kaushik S 

PROVIDER: S-EPMC3577913 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature