Name
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. |
Year | DOI | Venue |
|---|---|---|
2007 | 10.1093/bioinformatics/btm076 | BIOINFORMATICS |
Keywords | Field | DocType |
multiple alignment,protein domains,database search,protein sequence,conserved domain database,protein motif | Pairwise comparison,Data mining,Structural alignment,Alignment-free sequence analysis,Computer science,Conserved Domain Database,Bioinformatics,Multiple sequence alignment,PROSITE,Simple Modular Architecture Research Tool,Executable | Journal |
Volume | Issue | ISSN |
23 | 9 | 1367-4803 |
Citations | PageRank | References |
18 | 1.52 | 26 |
Authors | ||
2 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Jason S. Papadopoulos | 1 | 355 | 20.72 |
| Richa Agarwala | 2 | 310 | 58.02 |