NestedMICA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool NestedMICA
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Tool usage distribution map

This map represents all the scientific publications referring to NestedMICA per scientific context
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Protocols

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

Versioning


No version available

Publication for NestedMICA

NestedMICA citations

 (12)
library_books

MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome wide signatures

2015
BMC Genomics
PMCID: 4474412
PMID: 26099518
DOI: 10.1186/1471-2164-16-S7-S13

[…] s orthologous sequence alignments extracted from multiple genomes, and the other uses genome regions enriched with particular motifs in a single genome []. The first type of methods, such as MEME [], NestedMICA [], and Gibbs sampler [] utilize Bayesian model, EM algorithm, or Gibbs sampling techniques to obtain a Maximum A Posteriori (MAP) for motifs with a given length. Based on these methods, th […]

library_books

Motif discovery and transcription factor binding sites before and after the next generation sequencing era

2012
Brief Bioinform
PMCID: 3603212
PMID: 22517426
DOI: 10.1093/bib/bbs016

[…] : the expected frequency of an oligo is estimated by analyzing the oligos that appear at approximately the same distance from the genes transcription start site with a Bayesian segmentation algorithm.NestedMICA [] introduced mosaic background modeling. The idea is to use four different higher order background models according to the overall nucleotide composition of the input sequences, and in par […]

call_split

Genomic Targets of Brachyury (T) in Differentiating Mouse Embryonic Stem Cells

2012
PLoS One
PMCID: 3316570
PMID: 22479388
DOI: 10.1371/journal.pone.0033346
call_split See protocol

[…] n was applied to assess the significance of enrichment ratios. Target probes and surrounding promoter sequences were scanned for the published consensus in vitro T-box binding motif TCACACCT , using NestedMICA http://www.sanger.ac.uk/Software/analysis/nmica/index.shtml . We also used Regulatory Sequence Analysis Tools (RSAT) http://rsat.ulb.ac.be/rsat/ , to scan each target gene over a region −5 […]

library_books

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

2012
Cell
PMCID: 3368268
PMID: 22244452
DOI: 10.1016/j.cell.2011.11.058

[…] after exclusion of CTCF and NRSF/REST: length versus GERP Spearman's rho = 0.34, p value = 0.42; IC versus GERP rho = 0, p value = 1. Motif Discovery and Analysis Motif discovery was conducted with NestedMica using the parameters “-minLength 5 -maxLength 30 -numMotifs 6” and a fourth order background model trained on mammalian regulatory regions data. Discovered motifs were confirmed using MEME, […]

library_books

Computational biology for ageing

2011
PMCID: 3001313
PMID: 21115530
DOI: 10.1098/rstb.2010.0286

[…] find shared motifs across co-expressed genes, which could indicate a direct co-regulation by the same transcription factor. There are two general ways to address this: ab initio motif discovery (e.g. NestedMICA []) and library-based motif discovery (e.g. Clover []). The big advantage of ab initio methods is that they can discover novel motifs. However, motifs have to be strongly defined and/or ove […]

library_books

Metamotifs a generative model for building families of nucleotide position weight matrices

2010
BMC Bioinformatics
PMCID: 2906491
PMID: 20579334
DOI: 10.1186/1471-2105-11-348

[…] LE) Dirichlet distribution estimated from all the motif columns in the input data. It is computed with the optimisation procedure described in [].Our metamotif inference algorithm is a variant of the NestedMICA nested sampling algorithm described in detail in []. Nested sampling, originally introduced by [], is a generic Bayesian MCMC sampling strategy that allows drawing samples from a posterior […]


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

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