NestedMICA specifications

Information


Unique identifier OMICS_06280
Name NestedMICA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for NestedMICA

NestedMICA in publications

 (22)
PMCID: 4090240
PMID: 24983241
DOI: 10.1371/journal.pone.0101607

[…] for a common breakage-associated motif, we analyzed patient breakpoint regions and control sequences using multiple em for motif elicitation (meme) and nested motif independent component analysis (nestedmica). we also searched for repetitive dna with tandem repeats finder, quadparser, and repeatmasker. this large-scale analysis revealed an enrichment of tandem repeats and potential […]

PMCID: 4022013
PMID: 24555784
DOI: 10.1186/1745-6150-9-4

[…] motif found by setting all its occurrences to a special letter that cannot match any motif. then, the algorithm repeats the search for motifs []., dreme is much faster than meme [], weeder [], and nestedmica [,]. its runtime scales linearly with the size of the dataset []., meme-chip [] is a web service designed for analyzing chip-seq datasets and it is available from meme suite []. meme-chip […]

PMCID: 4056453
PMID: 24380390
DOI: 10.1186/gb-2013-14-12-r148

[…] among exactly six species (6) and shared among all seven species (7)) were further analyzed for diverse properties in each single species: ccat score (proportional to chip enrichment), the top nestedmica motif match score distribution (with 0 corresponding to the consensus motif), the numbers of peaks with at least one motif, overlaps with peaks called in distinct lcl cell lines […]

PMCID: 3757057
PMID: 24009522
DOI: 10.1371/journal.pgen.1003728

[…] 6,629 e14.5 peaks. we then ran ten different published motif discovery tools on the set of peaks and controls: allegro , alignace , bioprospetor , cisfinder , mdscan , meme , moan , motifsampler , nestedmica , and weeder . near identical motif predictions were combined. in a previous work we compiled a library of motifs (position weight matrices) for hundreds of different transcription factors […]

PMCID: 3744447
PMID: 23966877
DOI: 10.1371/journal.pgen.1003699

[…] tsss were uniquely associated with nee-activated genes. to identify putative regulatory elements that mediated transcriptional activation of inducible genes, we employed the motif-prediction tool nestedmica and analysed the +╬┤ac regions identified by chipseq in the cortex of mice exposed to nee. motif inference identified two elements of 20 and 29 bp (referred here as ac1 and ac2) […]


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NestedMICA institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

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