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COMA specifications

Information


Unique identifier OMICS_22007
Name COMA
Alternative name Comparison Of Multiple Alignments
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input data A protein sequence or multiple alignment.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ceslovas Venclovas <>

Information


Unique identifier OMICS_22007
Name COMA
Alternative name Comparison Of Multiple Alignments
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License Creative Commons Attribution-Noncommercial 3.0 Unported License
Computer skills Advanced
Version 1.10
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Ceslovas Venclovas <>

Publication for Comparison Of Multiple Alignments

COMA in publications

 (4)
PMCID: 5133447
PMID: 27906133
DOI: 10.1098/rsob.160249

[…] remote homologues using the more sensitive hmm–hmm comparison. hhalign (https://toolkit.tuebingen.mpg.de/hhalign []) was used for testing possible homology between eboa and ebog (see §3.2) by direct comparison of multiple alignments of eboa and ebog sequences (the alignments were built with mafft using sequences collected from the ncbi nr protein database with psi-blast)., the relationship […]

PMCID: 3673993
PMID: 23755117
DOI: 10.1371/journal.pone.0064194

[…] the genome between the origin of replication and orf v2 (position 14) and between orfs v3 and c3 (position 1841) in the genome with no effect on the integrity of orfs encoded by the virus. pairwise comparison of multiple alignments of individual orfs indicated that orfs encoded by grlav shared 99–100% and 98–100% identities at the nt and aa levels, respectively, with corresponding orfs of virus […]

PMCID: 2837030
PMID: 20158924
DOI: 10.1186/1471-2105-11-89

[…] improvement of profile-based methods. further development of statistical framework is another promising area of improvement for both profile and hmm-based methods., here, we present coma (comparison of multiple alignments), a new profile-profile search and comparison method that has a number of novel features. however, the two features that distinguish coma from other profile-profile […]

PMCID: 1891008
PMID: 17462020
DOI: 10.1111/j.1365-2958.2007.05688.x

[…] information from a pssm, hmm and amino-acid frequencies in the alignment to predict the secondary structure of syme (). the predicted structure was entirely congruent to that of the abrb fold (). comparison of multiple alignments of the syme family with classical members of the abrb superfamily indicated that they shared all the key hydrophobic residues, which constitute the core […]


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COMA institution(s)
Institute of Biotechnology, Vilnius, Lithuania
COMA funding source(s)
Supported by Lithuanian State Science and Studies Foundation and Howard Hughes Medical Institute.

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