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PhyloCon specifications

Information


Unique identifier OMICS_25392
Name PhyloCon
Alternative name Phylogenetic Consensus for Regulatory Motif Identification
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3b
Stability Stable
Source code URL http://stormo.wustl.edu/PhyloCon/PhyloCon-v3b.tar.gz
Maintained Yes

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Maintainer


  • person_outline Xiao-Dan Yu

Publication for Phylogenetic Consensus for Regulatory Motif Identification

PhyloCon citations

 (20)
library_books

Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co localization within regulatory modules

2016
BMC Bioinformatics
PMCID: 5117513
PMID: 27871221
DOI: 10.1186/s12859-016-1354-5

[…] (EMCMODULE, []). Instead, most newer programs combine phylogeny and possibly other information with TFBS patterns, either with consistent positioning (Stubb []; EMMA []; TWINE []) or without it ([]; PhyloCon []; CisPlusFinder []; cisTargetX [, ]). Programs searching a single genome for the consistent positional preferences within RMs are therefore surprisingly rare [].Notably, all our significant […]

library_books

A Systems View of the Differences between APOE ε4 Carriers and Non carriers in Alzheimer’s Disease

2016
PMCID: 4941795
PMID: 27462267
DOI: 10.3389/fnagi.2016.00171

[…] The conserved promoter motif(s) was/were identified by PhyloCon. PhyloCon, which stands for Phylogenetic Consensus, is one of the first motif-finding algorithms to combine the power of phylogenetic conservation and gene co-regulation (; ). PhyloCon first […]

library_books

Identifying Functional Transcription Factor Binding Sites in Yeast by Considering Their Positional Preference in the Promoters

2013
PLoS One
PMCID: 3873331
PMID: 24386279
DOI: 10.1371/journal.pone.0083791

[…] throughput RNA-seq method. Second, the genomic coordinates of 409,513 TFBSs of 122 yeast TFs were retrieved from MacIsaac et al.'s work , which used two well-known binding motif discovery algorithms, PhyloCon and Converge, to predict TFBSs and generate the position weight matrices (PWMs). Note that the retrieved TFBS dataset of a TF is a ranked list (sorted by the PWM values) of the predicted TFBS […]

library_books

Genome scale identification of cell wall related genes in Arabidopsis based on co expression network analysis

2012
BMC Plant Biol
PMCID: 3463447
PMID: 22877077
DOI: 10.1186/1471-2229-12-138

[…] sis could be as long as 1,000 bps as our data showed (Additional file : Figure S3a).For motif prediction, we used the following three prediction programs: WeederTFBS 1.4.2 [], MotifSampler 3a [,] and PhyloCon 3.2 []. These programs were selected because of their recognized strong performance as well as the complementary nature among the programs []. WeederTFBS allows the motif length to be 6, 8, 1 […]

call_split

A niched Pareto genetic algorithm for finding variable length regulatory motifs in DNA sequences

2011
3 Biotech
PMCID: 3376862
DOI: 10.1007/s13205-011-0040-6
call_split See protocol

[…] a motif’s significance into one probabilistic score. These aspects are overrepresentation of motifs and cross-species conservation of motifs. Wang and Stormo () developed 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 proba […]

library_books

A mutation degree model for the identification of transcriptional regulatory elements

2011
BMC Bioinformatics
PMCID: 3228546
PMID: 21708002
DOI: 10.1186/1471-2105-12-262

[…] was repeated for 5 times to reduce the sampling error.Since the tools of AlignACE, GLAM2, and Weeder were designed only to co-expressed genes, we only benchmark the performance of tools, PhyloGibbs, PhyloCon, WeederH and OCW here. Figure shows the result. Compared with the implementations of PhyloGibbs, PhyloCon and WeederH, OCW shows little variation with the increasing number of noisy sequence […]

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PhyloCon institution(s)
Department of Pathobiology, Center of Computational Biology, Institute of Basic Medical Sciences, Beijing, China

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