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GOMo specifications

Information


Unique identifier OMICS_08384
Name GOMo
Alternative name Gene Ontology for Motifs
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data DNA/RNA motifs
Operating system Unix/Linux
Computer skills Advanced
Version 4.10.1
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline FIMO Team

Information


Unique identifier OMICS_08384
Name GOMo
Alternative name Gene Ontology for Motifs
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data DNA/RNA motifs
Computer skills Basic
Version 4.10.1
Stability Stable
Maintained Yes

Maintainer


  • person_outline FIMO Team

Publication for Gene Ontology for Motifs

GOMo citations

 (12)
library_books

Evolutionary fates of universal stress protein paralogs in Platyhelminthes

2018
BMC Evol Biol
PMCID: 5793430
PMID: 29390964
DOI: 10.1186/s12862-018-1129-x

[…] n ATG. The Saccharomyces cerevisiae database was used to compare the identified motifs with others previously described (Tomtom) [], and to find associations with genes linked to gene ontology terms (GOMo) []. The motif search was executed with default parameters, considering a maximum width of 10 nucleotides and allowing any number of repetitions for the motifs in the sequence. All upstream seque […]

library_books

A comparative bioinformatic analysis of C9orf72

2018
PeerJ
PMCID: 5822839
PMID: 29479499
DOI: 10.7717/peerj.4391

[…] ined (). The TFs identified play an important role in the development of the nervous system including neuronal differentiation, migration and fate specification ().We also used MEME (), Tomtom () and GOMo (), three motif-based sequence analysis tools from the MEME suite of programs to analyse the upstream regulatory region in human, mouse and Fugu. MEME () identifies motifs based on the assumption […]

library_books

Genome wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori

2017
Sci Rep
PMCID: 5635003
PMID: 29018289
DOI: 10.1038/s41598-017-13186-6

[…] were identified by MEME (Fig. ). Short motifs without gaps were identified by DREME and similar motifs were predicted by TOMTOM. Motifs were annotated using the GoMo tool (http://meme-suite.org/tools/gomo). The network graphic used for motifs was generated by RAST. In the signal silk protein regulation mode analysis, we only used the report generated by JASPAR; the relative profile score was great […]

library_books

Genome wide profiling of S/MAR based replicon contact sites

2017
Nucleic Acids Res
PMCID: 5570033
PMID: 28609784
DOI: 10.1093/nar/gkx522

[…] in these regions common protein binding motifs with (G)GAGG or stretches of (T)4–11 occurred frequently (). These motifs were further analyzed for enrichment of associated GO terms using the web-tool Gene Ontology for Motifs (GOMo). Detected protein binding motifs within frequent contact sites of all three replicons were associated with GO terms binding, sequence-specific DNA binding, transcriptio […]

library_books

The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae)

2017
PeerJ
PMCID: 5571815
PMID: 28848689
DOI: 10.7717/peerj.3692

[…] (Echinoidea, Strongylocentrotidae). The list of the species used in the phylogenetic analysis and in the comparative analyses of DNA motifs, sequence similarity, and gene order are available in . The GOMo (Gene Ontology for Motifs; ) tool of the MEME suite was used to assign GO terms to the motifs discovered.The number of repeats in the LUR of the reference sample (F4) was calculated with tandem r […]

library_books

G quadruplex prediction in E. coli genome reveals a conserved putative G quadruplex Hairpin Duplex switch

2016
Nucleic Acids Res
PMCID: 5100583
PMID: 27596596
DOI: 10.1093/nar/gkw769

[…] g strand and the maximum number of columns to be aligned was set to 80, instead of the default value, 50. Because GLAM2 returns a non-compatible motif format to be used for the motif enrichment tool, GOMo, we also applied HPG1 and HPG2 to the MEME motif finder tool, both separately and combined (common motif) using the same parameters as mentioned for GLAM2. Motifs discovered from the MEME analysi […]

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GOMo institution(s)
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia

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