FIMO pipeline

FIMO specifications

Information


Unique identifier OMICS_05405
Name FIMO
Alternative name Find Individual Motif Occurrences
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data DNA/RNA/Protein motifs, DNA/Protein sequences
Operating system Unix/Linux
Computer skills Advanced
Version 4.10.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline FIMO Team <>

Information


Unique identifier OMICS_05405
Name FIMO
Alternative name Find Individual Motif Occurrences
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data DNA/RNA/Protein motifs, DNA/Protein sequences
Computer skills Basic
Version 4.10.1
Stability Stable
Maintained Yes

Maintainer


  • person_outline FIMO Team <>

Publication for Find Individual Motif Occurrences

FIMO citations

 (6)
2016
PMCID: 5135808

[…] obtained for the corresponding tf. the diff_log_pval_fimo binding score was defined as the logarithmic difference in the fimo p-value between the wild-type and mutant sequences, the avg_log_pval_fimo was calculated by averaging minus log of the two p-values, and the gain_or_loss was set to 1 (gain) or −1 (loss). on the contrary, when there was no motif change due to the mutation, […]

2016
PMCID: 4977670

[…] plants database [38], via its perl api (application program interface)., to predict tfbss in the upstream promoter regions, we installed a standalone version of the meme suite, which includes the fimo motif search tool [28, 39]. for this fimo motif discovery, we first collected a non-redundant set of position-weight matrices (pwms) for binding profiles of known tfs. briefly, we downloaded 64 […]

2016
PMCID: 4856318

[…] available in the jaspar database [85] to find the locations of the pwm motifs that are on the hypersensitive regions. we identified the locations of these pwm motifs on the hg38 assembly by using fimo [86] (p-value ≤10−5). we then intersected these motif locations with hypersensitive regions identified by the dnase-seq data for each tf. we repeated this process to identify active binding […]

2016
PMCID: 4841574

[…] chip-seq coverage as well as quality of immuno-precipitation. the affinity score, si,j, is defined as the -log10(p-value) of motif match with highest score in region i. motif scan is performed using fimo [51]. a affinity score of 2 was given to regions without any motif match., we assume binding affinity to the sequence decreases monotonically with motif p-value. the p-value indicates […]

2016
PMCID: 4889651

[…] corresponding regions of all c. reinhardtii genes. fimo (find individual motif occurrences; grant et al. 2011) was used to count occurrences of the zyre motif in different sequence sets. segmented fimo frequencies were tested statistically using student’s t-test to assess enrichment in zygotic genes vs. a background null model composed of sequences from all gene models., luciferase reporter […]

FIMO institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
FIMO funding source(s)
This work was supported by National Institutes of Health award 2 R01 RR021692.

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