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FIRE specifications

Information


Unique identifier OMICS_21739
Name FIRE
Alternative name Finding Informative Regulatory Elements
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Maintained No

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Additional information


https://tavazoielab.c2b2.columbia.edu/FIRE/tutorial.html

Publication for Finding Informative Regulatory Elements

FIRE in publications

 (14)
PMCID: 5908064
PMID: 29672507
DOI: 10.1371/journal.pbio.2004979

[…] long reversals were counted as avoidance []. the tests were done at least 5 times with 10 animals each., motif discovery was carried out using information-theoretic analysis as implemented in the finding informative regulatory elements (fire) algorithm []. de novo motifs were discovered by running fire in discrete mode, with all the genes in the c. elegans genome labeled as either belonging […]

PMCID: 5765359
PMID: 29158339
DOI: 10.1534/g3.117.300415

[…] in the dhh1 go term finder output were submitted to go slim mapper using default settings (http://www.yeastgenome.org/cgi-bin/go/goslimmapper.pl)., sequence motifs were identified using fire (finding informative regulatory elements), which was performed either locally or on the iget website (https://iget.c2b2.columbia.edu) using default settings to analyze “discrete” or “continuous” data […]

PMCID: 5238449
PMID: 28091569
DOI: 10.1038/srep40655

[…] in gene expression and chromatin structure of cvgs we identified putative binding sites for ap2 transcription factors on differentially expressed genes during the mosquito life cycle. we used the finding informative regulatory elements (fire) algorithm, which searches for motifs whose presence or absence is highly informative of the associated expression values. this analysis reveals […]

PMCID: 4852458
PMID: 27249342
DOI: 10.1098/rsob.160003

[…] correlated with their unique regulatory functions., the question is how this region-specific methylation is targeted. bioinformatic analysis of merip-seq data using the motif discovery algorithm finding informative regulatory elements (fire) identified the predominant consensus motifs of m6a: g [g/a] m6acu and related variants ([ac]gac[gu], ggac, [au][cg]g[ag]ac and ugac), and almost 90% […]

PMCID: 4322800
PMID: 25652008
DOI: 10.1186/s13071-015-0701-0

[…] if we are to effectively design in vitro studies to validate this role., we report here the application of a repeated search of variations of 5′ flanking sequences from p. falciparum using the finding informative regulatory elements (fire) algorithm., our approach repeatedly found a short-list of high scoring dna motifs, for which cognate specific transcription factors were available, […]


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FIRE institution(s)
Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ, USA
FIRE funding source(s)
Supported by grants from NIH and NSF.

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