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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

Versioning


No version available

Maintainers


This tool is not maintained anymore.

Additional information


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

Publication for Finding Informative Regulatory Elements

FIRE citations

 (7)
library_books

Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae

2017
Sci Rep
PMCID: 5238449
PMID: 28091569
DOI: 10.1038/srep40655

[…] ons 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 that spor […]

library_books

Recent advances in dynamic m6A RNA modification

2016
Open Biol
PMCID: 4852458
PMID: 27249342
DOI: 10.1098/rsob.160003

[…] mately 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% of a […]

library_books

Triaging informative cis regulatory elements for the combinatorial control of temporal gene expression during Plasmodium falciparum intraerythrocytic development

2015
PMCID: 4322800
PMID: 25652008
DOI: 10.1186/s13071-015-0701-0

[…] The Finding Informative Regulatory Elements (FIRE) algorithm discovers DNA motifs whose presence or absence in gene flanking sequences provides the most information about the expression profile of the ass […]

library_books

Investigation of protein secretion and secretion stress in Ashbya gossypii

2014
BMC Genomics
PMCID: 4320514
PMID: 25523110
DOI: 10.1186/1471-2164-15-1137

[…] R-package ‘GOstats’ [] was used to analyse gene expression correlation and co-expression clusters and REVIGO [] was used to summarize the GO term lists.Promoter sequences were analysed with the tool Finding Informative Regulatory Elements (FIRE) [], with default settings using the A. gossypii genome. Co-expression clusters and clusters of differentially expressed genes were used as groups of gene […]

library_books

Finding the target sites of RNA binding proteins

2013
PMCID: 4253089
PMID: 24217996
DOI: 10.1002/wrna.1201

[…] orithm originally designed to find repeated, ungapped sequence patterns in DNA or proteins. MEME has been used to predict motifs for Puf proteins in flies and yeast., Additional models, such as FIRE (finding informative regulatory elements) and REFINE (relative filtering by nucleotide enrichment), have been used to identify a group of sequence consensuses from yeast RIP-Chip datasets. Motif finder […]

library_books

Genome wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile

2013
BMC Genomics
PMCID: 3734150
PMID: 23895416
DOI: 10.1186/1471-2164-14-516

[…] Upstream regions of genes present in each cluster were analyzed for de novo patterns using 3 pattern-finding algorithms: Multiple EM for Motif Elicitation (MEME) []; AlignACE [] and Finding Informative Regulatory Elements (FIRE) algorithm [].MEME was run using the parameters minw=7, maxw=20, in two modes (zoops & anr) and the significant motifs (E-value >= 1e-01) for each cluster […]


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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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