BioMart protocols

BioMart specifications

Information


Unique identifier OMICS_03841
Name BioMart
Interface Web user interface
Restrictions to use None
Programming languages R
License Artistic License version 2.0
Computer skills Basic
Version 2.30.0
Stability Stable
Requirements methods
Maintained Yes

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Documentation


Maintainer


  • person_outline Arek Kasprzyk <>

Publications for BioMart

BioMart IN pipelines

 (7)
2017
PMCID: 5741957
PMID: 29273003
DOI: 10.1186/s12863-017-0584-5

[…] sorghum drought responsive orthologs were identified in three species namely arabidopsis, rice and maize (additional file 10) and were retrieved from the ensembl compara database using ensembl biomart [31]., percent identity and orthology confidence levels were used as parameters to retrieve matching orthologs. all available homology types (one2one, one2many and many2many) […]

2016
PMCID: 4889651
PMID: 27172209
DOI: 10.1534/g3.116.029181

[…] gene models used for sequence retrieval were downloaded from phytozome 10 (v5.5, doe joint genome institute; http://phytozome.jgi.doe.gov; merchant et al. 2007; blaby et al. 2014) using the biomart platform (smedley et al. 2009). individual portions of genes [500 bp upstream of start codons for gene models, upstream regions to transcription start sites (tsss), 5′-/3′-utrs, whole gene […]

2016
PMCID: 4889651
PMID: 27172209
DOI: 10.1534/g3.116.029181

[…] of genes [500 bp upstream of start codons for gene models, upstream regions to transcription start sites (tsss), 5′-/3′-utrs, whole gene models and coding sequences (cdss)] were retrieved using biomart. meme (multiple expectation maximization for motif elicitation; bailey and elkan 1994) was used to find enriched motifs in the 500 bp regions upstream of cdss for the 300 most highly […]

2015
PMCID: 4652402
PMID: 26581338
DOI: 10.1186/s12964-015-0121-y

[…] between nuleotide or protein sequences, which can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene familiesbiomart http://www.biomart.org [93]provides free software and data services to foster scientific collaboration and facilitate the scientific discovery proces; the project adheres to the open source philosophy […]

2014
PMCID: 4303946
PMID: 25563934
DOI: 10.1186/1471-2164-15-S12-S5

[…] to the categories of "biological processes" "biological functions" and "structural components." getting the gene ontology for the lists of considered genes was performed with the use of r package biomart [23,24]. analysis of the gene ontologies overlapping for different influencing factors was carried out in the r package venndiagram [25]. statistical significance and visualization of gene […]

BioMart institution(s)
Department of Electronical Engineering, ESAT-SCD, K.U.Leuven, Leuven-Heverlee, Belgium; EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Cancer Genetics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
BioMart funding source(s)
This work was supported by PhD/postdoctoral grants, projects G.0115.01, G.0413.03, G.0388.03, G.0229.03, research communities (ICCoS, ANMMM, MLDM); PhD Grants, GBOUSQUAD, GBOU-ANA, GBOU-McKnow, STWW-Genprom; Belgian Federal Government: DWTC IUAP V-22; EU: FP5, CAGE, ERNSI; German Ministry for Education and Research through National Genome Research Network (NGFN) grant FKZ 01GR0450.

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