PhyME protocols

View PhyME computational protocol

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Associated diseases

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PhyME specifications

Information


Unique identifier OMICS_06273
Name PhyME
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PhyME

PhyME in pipeline

2017
PMCID: 5333389
PMID: 28249564
DOI: 10.1186/s12859-017-1495-1

[…] generation sequencing and the resulting avalanche of data [–]., examples for highly popular phylogenetic footprinting tools that have been applied to eukaryotes and prokaryotes are footprinter [], phyme [], monkey [], microfootprinter [], phylogenetic gibbs sampler [], phylogibbs [], phylogibbs-mp [], or motevo []., in summary, one-species approaches neglect phylogenetic information, whereas […]


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PhyME in publications

 (20)
PMCID: 5333389
PMID: 28249564
DOI: 10.1186/s12859-017-1495-1

[…] generation sequencing and the resulting avalanche of data [–]., examples for highly popular phylogenetic footprinting tools that have been applied to eukaryotes and prokaryotes are footprinter [], phyme [], monkey [], microfootprinter [], phylogenetic gibbs sampler [], phylogibbs [], phylogibbs-mp [], or motevo []., in summary, one-species approaches neglect phylogenetic information, whereas […]

PMCID: 5447242
PMID: 28130227
DOI: 10.1093/bioinformatics/btx033

[…] approaches for de-novo motif discovery based on phylogenetic footprinting have become increasingly attractive. examples of highly popular tools for phylogenetic footprinting are footprinter (), phyme (), monkey (), phylogibbs (), phylogenetic gibbs sampler (), phylogibbs-mp () and motevo (). provides a comparison of these tools regarding the used evolutionary model, sequence model […]

PMCID: 5014158
PMID: 27436282
DOI: 10.1093/jxb/erw275

[…] 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 increase […]

PMCID: 3764189
PMID: 24039608
DOI: 10.1371/journal.pgen.1003772

[…] of these genes and their orthologs for occurrences of the sequence rtgggaa, which has previously been shown to be bound by lag-1 . we conducted pairwise alignments of these upstream regions using phyme to identify conserved sequence blocks (regions of at least 14 nt with at least 70% identity). we considered a predicted lag-1/csl sequence conserved if it aligned to blocks containing rtgggaa […]

PMCID: 3376862
DOI: 10.1007/s13205-011-0040-6

[…] the motif finding algorithm phylocon that takes into account both aspects, conservation among orthologous genes and co-regulation of genes within a species. sinha et al. () developed the algorithm phyme that was based on a probabilistic approach. this algorithm handles data from promoters of co-regulated genes and orthologous sequences., according to reference (chan et al. ), the motif […]


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PhyME institution(s)
Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA

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