COBALT: constraint-based alignment tool for multiple protein sequences
By Jason S. Papadopoulos, Richa Agarwala. Bioinform., 2007
1,128 citations recorded by the source corpus.
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
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/04539657665c0302820f1592ab7a88a3c4b15b6b
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In Materials Chemistry
In Molecular Biology
- Rodolphe Barrangou
- Kazutaka Katoh
- Hiroyuki Toh
- V. Šikšnys
- G. Gasiunas
- Philippe Horvath
- Feng Zhang
- C. Fremaux
Citations in the corpus
- Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (2008, background): “Moreover, the accuracy of multiple alignment is improved by using information of homologs, probably because homologs make family-specific information available and enrich the profiles used in the multiple alignment processes [20-26].”
- RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation (2020, methodology): “The table of proteins can be downloaded, proteins can be selected for FASTA or document summary download, or subjected to multiple sequence alignment with COBALT (19).”
- The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli (2011, methodology): “Alignments were assemled using “COBALT” (1) tool and visualised with “BioEdit 7.”
- Predicting Functionally Informative Mutations in Escherichia coli BamA Using Evolutionary Covariance Analysis (2013, background): “…that are separated by Loop 6 (G631V, G631W, F718L); the extracellular end of b 10 (E607A); b 1 (T423I), and the C-terminal POTRA domain (P5) within the periplasmic extension (F395V) (Figure 2, green; see Figure S2 for POTRA alignment) (Papadopoulos and Agarwala 2007; Jacob-Dubuisson et al. 2009).”