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ORCAtk specifications

Information


Unique identifier OMICS_12905
Name ORCAtk
Alternative name ORCA toolkit
Interface Web user interface
Restrictions to use None
Input data Gene symbol/name, genomic sequence
Output data Summary, plot file
Output format PNG
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Basic
Version 1.0.0
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Wyeth Wasserman <>

Information


Unique identifier OMICS_12905
Name ORCAtk
Alternative name ORCA toolkit
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data Gene name/symbol, genomic sequence
Output data Summary, plot file
Output format PNG
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Wyeth Wasserman <>

Publication for ORCA toolkit

ORCAtk in pipeline

2017
PMCID: 5215532
PMID: 28052101
DOI: 10.1371/journal.pone.0169237

[…] on roadmap datasets., these hypothesized regulatory regions were then queried for transcription factor binding sites, based on known and predicted tf binding sites and motifs. we used both the orca toolkit web server and the meme suite of motif analysis applications to isolate highly conserved (>80% phastcons score) sub-regions within these hypothesized regulatory regions, […]


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ORCAtk in publications

 (3)
PMCID: 5215532
PMID: 28052101
DOI: 10.1371/journal.pone.0169237

[…] chromatin-associated rna-seq reads from patterson et al. and mirna gene transcripts in cells lacking dgcr8 from chang et al6,25.transcription factor binding site predictions were performed with the orca toolkit web server, and with the meme suite of motif analysis applications45,46., the encode and epigenetic roadmap datasets, with accession numbers listed in tables and , contain mapped reads […]

PMCID: 4512088
PMID: 26204903
DOI: 10.1186/s12864-015-1770-3

[…] genes containing nr2e1 binding sites within their promoter regions. thus, interrogation of our pooled list of 1279 refseq accession numbers was undertaken using three different software tools; the orca toolkit (tk) to perform the initial orthologous-sequence alignment and phylogenetic footprinting [], a customized version of opossum for prediction and storage of transcription factor binding […]

PMCID: 3239227
PMID: 21989199
DOI: 10.1186/gm281

[…] dna sequence. software for scanning dna sequences using the matrix models is widely available through computer programming modules (tfbs []), downloadable software (rsat []) or online websites (orcatk []). active discussions are ongoing in the bioinformatics field about how the models can be improved in light of the increasing amount of tfbs data arising from chip-seq studies []., pssms […]


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ORCAtk institution(s)
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Applied Genomics Department, Pharmaceutical Research Institute, Bristol-Myers Squibb, NJ, USA
ORCAtk funding source(s)
GenomeCanada (via the Pleiades Promoter Project to PAZAR and ORCAtk); the Canadian Institute of Health Research; Canada Foundation for Innovation, the Canadian Genetic Diseases Network; Merck and IBM

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