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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sadreyev RI,Tang M,Kim BH,Grishin NVdoi
10.1093/nar/gkm293subject
Has Abstractpub_date
2007-07-01 00:00:00pages
W653-8issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkm293journal_volume
35pub_type
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