COMPASS server for remote homology inference

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 inp...

• Type: Journal
• Year: 2007
• Where: NAR
• Authors: Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin
• Keywords: Homology Detection, Local Profile-profile Alignments, Multiple Sequence Alignments, NAR 2007