The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
COBALT: constraint-based alignment tool for multiple protein sequences
Open accessAbstract
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
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Cites
CDD: a Conserved Domain Database for protein classification
Marchler-Bauer, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki069 · Cited by 1,156
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Coordinators, N. R. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1071 · Cited by 817
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Sayers, E. W., Barrett, T., Benson, D. A., Bolton, E., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Federhen, S., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp967 · Cited by 804
Metadata
- Authors
- Papadopoulos, J. S., & Agarwala, R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-03-01
- Volume
- 23
- Issue
- 9
- Pages
- 1073-1079
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2162800127
- Cited by
- 1,127
- References
- 1
- FWCI
- 3.71
- Type
- journal article
- Language
- en
- Open access
- hybrid
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