COMPASS server for remote homology inference

Ruslan I. Sadreyev, Ming Tang, Bong Hyun Kim, Nick V. Grishin

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

COMPASS is a method for homology detection and local alignment construction based on the comparison of multiple sequence alignments (MSAs). The method derives numerical profiles from given MSAs, constructs local profile-profile alignments and analytically estimates E-values for the detected similarities. Until now, COMPASS was only available for download and local installation. Here, we present a new web server featuring the latest version of COMPASS, which provides (i) increased sensitivity and selectivity of homology detection; (ii) longer, more complete alignments; and (iii) faster computational speed. After submission of the query MSA or single sequence, the server performs searches versus a user-specified database. The server includes detailed and intuitive control of the search parameters. A flexible output format, structured similarly to BLAST and PSI-BLAST, provides an easy way to read and analyze the detected profile similarities. Brief help sections are available for all input parameters and output options, along with detailed documentation. To illustrate the value of this tool for protein structure-functional prediction, we present two examples of detecting distant homologs for uncharacterized protein families. Available at http://prodata.swmed.edu/compass.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume35
Issue numberSUPPL.2
DOIs
StatePublished - Jul 2007

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Sequence Alignment
Documentation
Proteins
Databases

ASJC Scopus subject areas

  • Genetics

Cite this

COMPASS server for remote homology inference. / Sadreyev, Ruslan I.; Tang, Ming; Kim, Bong Hyun; Grishin, Nick V.

In: Nucleic Acids Research, Vol. 35, No. SUPPL.2, 07.2007.

Research output: Contribution to journalArticle

Sadreyev, Ruslan I. ; Tang, Ming ; Kim, Bong Hyun ; Grishin, Nick V. / COMPASS server for remote homology inference. In: Nucleic Acids Research. 2007 ; Vol. 35, No. SUPPL.2.
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