COBALT: constraint-based alignment tool for multiple protein sequences
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ID: 297780
2007
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Abstract
Abstract Motivation: A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools. Results: We describe COBALT, a constraint based alignment tool that implements a general framework for multiple alignment of protein sequences. COBALT finds a collection of pairwise constraints derived from database searches, sequence similarity and user input, combines these pairwise constraints, and then incorporates them into a progressive multiple alignment. We show that using constraints derived from the conserved domain database (CDD) and PROSITE protein-motif database improves COBALT's alignment quality. We also show that COBALT has reasonable runtime performance and alignment accuracy comparable to or exceeding that of other tools for a broad range of problems. Availability: COBALT is included in the NCBI C++ toolkit. A Linux executable for COBALT, and CDD and PROSITE data used is available at: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/cobalt Contact: richa@helix.nih.gov
| Reference Key |
openalex_W2162800127
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|---|---|
| Authors | Jason S. Papadopoulos, Richa Agarwala |
| Journal | BMC Bioinformatics |
| Year | 2007 |
| DOI |
10.1093/bioinformatics/btm076
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| URL | |
| Keywords | Keywords not found |
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