OMA pipeline

OMA specifications

Information


Unique identifier OMICS_01690
Name OMA
Alternative name Orthologous MAtrix
Software type Application/Script
Interface Command line interface, Web user interface
Restrictions to use None
Input data A genome and some parameters.
Input format FASTA+Drawin
Output format TXT
Operating system Unix/Linux
License Mozilla Public License version 2.0
Computer skills Advanced
Version 2.1.1
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Orthologous_MAtrix

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Maintainers


  • person_outline OMA Team <>
  • person_outline Christophe Dessimoz <>

Additional information


https://omabrowser.org/oma/about/ A standalone version of the web browser is available at https://omabrowser.org/standalone/

Publications for Orthologous MAtrix

OMA IN pipelines

 (2)
2016
PMCID: 5062322
PMID: 27501943
DOI: 10.1093/molbev/msw164

[…] as alpha helices and 80 as beta barrels), 378 of which unambiguously specified inside- versus outside-facing aqueous regions. homologs were procured by blastp search against a local subset of the oma database created as described earlier, and alignments produced with mafft. to “slice” (i.e., split vertically) the multiple-sequence alignments (msas) used in figure 5e and supplementary figures […]

2016
PMCID: 5359404
PMID: 28348828
DOI: 10.1099/mgen.0.000081

[…] that also did not have corresponding peaks in a dna only (chip with flag antibody in wt background) control (zhang et al., 2008)., orthologues of r. capsulatus in r. sphaeroides were found using the oma orthology database, accessible at http://http://www.omabrowser.org (altenhoff et al., 2015)., genes directly and indirectly regulated by rega were identified by performing rna-seq analyses […]

OMA institution(s)
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; ETH Zurich, Computer Science, Zurich, Switzerland; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Department of Genetics, Evolution & Environment, University College London, London, UK; Bayer Crop Science NV, Gent, Belgium; Department of Computer Science, University College London, London, UK
OMA funding source(s)
Supported by Swiss Institute of Bioinformatics, Service and Infrastructure grant; UK Biotechnology and Biological Sciences Research Council [BB/L018241/1, BB/M009513/1]; University College London, UCL Impact Award; Bayer Crop Science NV.

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