COMA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool COMA
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Tool usage distribution map

This map represents all the scientific publications referring to COMA per scientific context
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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 citations

 (4)
library_books

The plastid genome of some eustigmatophyte algae harbours a bacteria derived six gene cluster for biosynthesis of a novel secondary metabolite

2016
Open Biol
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 of EboB […]

library_books

A Leafhopper Transmissible DNA Virus with Novel Evolutionary Lineage in the Family Geminiviridae Implicated in Grapevine Redleaf Disease by Next Generation Sequencing

2013
PLoS One
PMCID: 3673993
PMID: 23755117
DOI: 10.1371/journal.pone.0064194

[…] f 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 […]

library_books

Detection of distant evolutionary relationships between protein families using theory of sequence profile profile comparison

2010
BMC Bioinformatics
PMCID: 2837030
PMID: 20158924
DOI: 10.1186/1471-2105-11-89

[…] considerable 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 c […]

library_books

An antisense RNA controls synthesis of an SOS induced toxin evolved from an antitoxin

2007
Mol Microbiol
PMCID: 1891008
PMID: 17462020
DOI: 10.1111/j.1365-2958.2007.05688.x

[…] the 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 of this foldi […]


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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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