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STEME specifications

Information


Unique identifier OMICS_06295
Name STEME
Alternative name Suffix Tree EM for Motif Elicitation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.9.4
Stability Stable
Maintained Yes

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Maintainer


  • person_outline John Reid

Information


Unique identifier OMICS_06295
Name STEME
Alternative name Suffix Tree EM for Motif Elicitation
Interface Web user interface
Restrictions to use None
Input data Some sequences files.
Input format FASTA
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline John Reid

Publications for Suffix Tree EM for Motif Elicitation

STEME citations

 (7)
library_books

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets

2018
Nucleic Acids Res
PMCID: 5934673
PMID: 29385521
DOI: 10.1093/nar/gky027

[…] tic algorithm with EM to improve starting PPMs, SEME () which uses importance sampling to speed-up the search, EXTREME () which achieves speed-up by using the on–line version of the EM algorithm, and STEME () which resorts to suffix-trees. Moreover, Liu et al. () use Gibbs sampling and Ikebata and Yoshida () use a repulsive MCMC version of MEME type search for simultaneous discovery of several mot […]

library_books

ATF3 negatively regulates cellular antiviral signaling and autophagy in the absence of type I interferons

2017
Sci Rep
PMCID: 5562757
PMID: 28821775
DOI: 10.1038/s41598-017-08584-9

[…] bmitted post peak calling on GEO) and identified the genes with a binding signal in +/− 10 kb of gene promoters. Also, we used the sequence of binding sites to predict the binding motif of ATF3 using STEME and then scanned the obtained motif to identify other possible binding sites of ATF3. After that, we intersected the two gene lists to identify genes that could be potentially regulated by ATF3. […]

library_books

Genome wide analysis reveals positional nucleosome oriented binding pattern of pioneer factor FOXA1

2016
Nucleic Acids Res
PMCID: 5027512
PMID: 27458208
DOI: 10.1093/nar/gkw659

[…] To examine if the identified BCSs contain the canonical FOXA1 binding motif and whether they include other possible TF binding motifs, we have performed a de-novo motif discovery by STEME () and motif scanning by FIMO (). We defined the binding regions used for the motif discovery and scanning based on the following rules: for the SPBS mode, a 45 bp DNA sequence with 15 bp upstre […]

library_books

A Fast Cluster Motif Finding Algorithm for ChIP Seq Data Sets

2015
Biomed Res Int
PMCID: 4509496
PMID: 26236718
DOI: 10.1155/2015/218068

[…] hile ignoring the remaining unselected sequences. That decreases the chance of discovering motifs related to infrequent cofactors. Meanwhile, PWM-based methods also have been developed. For instance, STEME [] applies suffix trees to accelerate EM steps. This strategy acts well in case of finding short motifs. However, it executes much slower when the width of motif increases in the large data set. […]

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

[…] . In addition, due to the probabilistic nature of the models, they are more or less sensitive to noises in input data. Efforts have been made to improve these classic methods over the last few years. STEME [] speeds up MEME by indexing sequences with a suffix tree. ChIPMunk [] searches a gapless multiple local alignment using a greedy algorithm to deal with a large set of inputs.On the other hand, […]

library_books

De novo prediction of cis regulatory elements and modules through integrative analysis of a large number of ChIP datasets

2014
BMC Genomics
PMCID: 4265420
PMID: 25442502
DOI: 10.1186/1471-2164-15-1047

[…] a motif-finding tool [, ]. Although a few new motif-finders have been developed to analyze large sequence sets from ChIP-seq experiments, such as seeder [], Trawler [, ], ChIPMunk [], HMS [], CMF [], STEME [], DREME [], DECOD [], RSAT [], and POSMO [], they are typically used to find the CREs of a ChIP-ed TF in a short region of sequences (~200 bp) around the binding peak summits in order to reduc […]

Citations

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STEME institution(s)
MRC Biostatistics Unit, Institute of Public Health, Cambridge, UK
STEME funding source(s)
Supported by the Medical Research Council Unit Programme number U105260799.

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