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Phyloscan specifications


Unique identifier OMICS_10965
Name Phyloscan
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Maintained No


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Publications for Phyloscan

Phyloscan citations


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

J Exp Bot
PMCID: 5014158
PMID: 27436282
DOI: 10.1093/jxb/erw275

[…] can be categorized into three major classes: (1) methods based on position weight matrix (PWM), e.g. TRAP (), MATCH (), 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 i […]


Epitopes of Microbial and Human Heat Shock Protein 60 and Their Recognition in Myalgic Encephalomyelitis

PLoS One
PMCID: 3842916
PMID: 24312270
DOI: 10.1371/journal.pone.0081155

[…] n samples than the G20 peptide. It was therefore chosen as the basis for further investigations.In an extension of the epitope scanning we compared peptides homologous with the human G20c peptide, a “phyloscan”. Certain ME and BD samples gave high IgG and IgM antibody reactions to HSP60 peptides from Leishmania and Schistosoma. Like Plasmodium, these microbes are rare in Sweden. The highly conserv […]


A survey of DNA motif finding algorithms

BMC Bioinformatics
PMCID: 2099490
PMID: 18047721
DOI: 10.1186/1471-2105-8-S7-S21

[…] than 90% of known transcription factor binding sites. They claimed that this algorithm can be applied to much larger genome such as the human genome.Carmack et al. [] developed a scanning algorithm, PhyloScan, which combines evidence from matching sites found in orthologous data from several related species with evidence from multiple sites within an intergenic region, to better detect regulons. […]

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Phyloscan institution(s)
Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, USA; Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY, USA
Phyloscan funding source(s)
National Science Foundation (CCF0914739); Department of Energy (DE-SC000592); National Institutes of Health (5K25HG003291); Wadsworth Center Bioinformatics Core

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