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Protocols

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

Versioning


No version available

Maintainer


  • person_outline Martin Tompa <>

Publication for YMF

YMF citations

 (12)
library_books

Systems analysis of cis regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de etiolation

2016
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 […]

library_books

A Genome Wide Screen of CREB Occupancy Identifies the RhoA Inhibitors Par6C and Rnd3 as Regulators of BDNF Induced Synaptogenesis

2013
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 […]

library_books

Genome wide Prediction and Functional Validation of Promoter Motifs Regulating Gene Expression in Spore and Infection Stages of Phytophthora infestans

2013
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 […]

library_books

ChIP seq and transcriptome analysis of the OmpR regulon of Salmonella enterica serovars Typhi and Typhimurium reveals accessory genes implicated in host colonization

2012
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 […]

library_books

AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses

2011
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 […]

library_books

A highly efficient and effective motif discovery method for ChIP seq/ChIP chip data using positional information

2011
PMCID: 3326300
PMID: 22228832
DOI: 10.1093/nar/gkr1135

[…] program can be freely downloaded from http://cb.utdallas.edu/posmo/index.html., we first used simulation to compare our posmo algorithm with established methods, such as exhaustive enumeration [e.g. ymf (), dwe () and dme ()] and iterative optimization [e.g. meme ()]. we decided to compare our algorithm with dme and meme as representatives of the above two categories. as it turned out, […]


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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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