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YMF specifications

Information


Unique identifier OMICS_06277
Name YMF
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequences
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Martin Tompa <>

Publication for YMF

YMF in pipeline

2011
PMCID: 3171486
PMID: 21931761
DOI: 10.1371/journal.pone.0024576

[…] this is the maximal motif length allowed. the motif length for mdscan was set to 12 and 20, respectively. to control the total running time with limited computational resources, the motif length for ymf, moan and dme were set to 12. for meme, the minimal and maximal motif lengths are set to 12 and 20, respectively. amd and spacer both automatically selected significant motifs of the appropriate […]

YMF in publications

 (12)
PMCID: 5014158
PMID: 27436282
DOI: 10.1093/jxb/erw275

[…] and signal scan (); (2) phylogenetic footprinting methods, e.g. footprinter (), phyloscan (), and phyme (); and (3) standard motif-finding algorithms, e.g. gibbs sampling (), meme (), alignace (), ymf (), and weeder (). it is a common practice to combine different approaches to increase the reliability and decrease the false discovery rates of the prediction., in this study, we aimed […]

PMCID: 3675129
PMID: 23762244
DOI: 10.1371/journal.pone.0064658

[…] motif analyses utilized 500 bp regions flanking the sequence tag center of mass of the top 1000 chip-seq peaks with and without the canonical cre (ranked by total sequence counts). the weeder and ymf algorithms produced similar results using flags that allowed for the presence of more than one 6- mer motif on both strands , . statistical analyses and visualization of motif data utilized […]

PMCID: 3597505
PMID: 23516354
DOI: 10.1371/journal.ppat.1003182

[…] were then tested for positional bias, orientation bias, and evolutionary conservation., each of the five stage-induced datasets were searched separately for motifs using bioprospector, meme, and ymf. these programs were selected since they employ independent methods and scored well in prior comparisons , . we focused on promoters from genes induced >10-fold between developmental […]

PMCID: 3586657
PMID: 23190111
DOI: 10.1111/mmi.12111

[…] or known cds were ignored unless there were multiple similar sites nearby, reducing the total number of analysed peaks to 43. enriched sequences were then input to the motif finding algorithm ymf with the length of motif set to eight nucleotides and with a maximum of two redundant bases ()., rna was extracted from s. typhi using a fast rna blue kit (mp biomedicals) according […]

PMCID: 3171486
PMID: 21931761
DOI: 10.1371/journal.pone.0024576

[…] the potential motifs to be discovered. numerous de novo motif discovery tools have been recently developed and quickly adapted by investigators in the community, including alignace , reduce , meme , ymf , mdscan , weeder , dme and trawler . despite these available tools, the effective and efficient identification of motifs within datasets of interest remains a challenging problem, particularly […]

YMF institution(s)
Center for Studies in Physics and Biology, The Rockefeller University, NY, NY, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA

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