Tools for MOtif Discovery in nucleotide sequences
NEW Weeder (version: 2.0)
Motif (transcription factor binding sites) discovery in sequences from coregulated genes of a single species.
This is a new Weeder release rewritten to be faster and optimized for large ChIP-Seq data.
NEW PscanChIP (version: 1.1) NEW
Motif (transcription factor binding sites) discovery in sequences from ChIP-Seq experiments using JASPAR and TRANSFAC matrices.
F.Zambelli, G.Pesole, G.Pavesi
PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.
Nucleic Acids Research 2013 41(W1): W535-W543.
Cscan (version: 1.2)
Finding transcription factors regulating a set of genes
using binding data from a large collection of ChIP-Seq experiments in human and mouse.
F.Zambelli, G.M.Prazzoli, G.Pesole, G.Pavesi
Cscan: Finding Common Regulators of a set of Genes by Using a Collection of Genome-Wide ChIP-Seq Datasets
Nucleic Acids Research, 2012 40(W1): W510-W515.
Pscan (version: 1.3)
Motif (transcription factor binding sites) discovery in sequences from co-regulated genes using JASPAR and TRANSFAC matrices.
To learn more:
F.Zambelli, G.Pesole, G.Pavesi
Finding Over-represented Transcription Factor Binding Site Motifs in Sequences from Co-Regulated or Co-Expressed Genes.
Nucleic Acids Research 2009 37(Web Server issue):W247-W252.
Weeder (version: 1.4.2)
Motif (transcription factor binding sites) discovery in sequences from coregulated genes of a single species.
WeederH (version: 1.0)
Motif (TFBSs) and regulatory region (CRM) discovery in sequences from homologous genes. To learn more:
G.Pavesi, F.Zambelli, G.Pesole. WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinformatics 2007, 8:46
RNAprofile (version: 2.2)
Secondary structure motif discovery in RNA sequences
References:
Overall: Pavesi, G., Mereghetti, P., Zambelli, F., Stefani, M., Mauri, G., Pesole, G.
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
Nucleic Acids Res 2006 34:W566-W570
and
Zambelli, F., Pesole, G., Pavesi, G.
Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences.
Current Protocols in Bioinformatics 2014 Sep 8;47:2.11.1-2.11.31
WeederH: Pavesi, G., Zambelli, F., Pesole, G.
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences.
BMC Bioinformatics 2007, 8:46
Pscan: F.Zambelli, G.Pesole, G.Pavesi
PScan: Finding Over-represented Transcription Factor Binding Site Motifs in Sequences from Co-Regulated or Co-Expressed Genes.
Nucleic Acids Research 2009 37(Web Server issue):W247-W252.
Cscan: F.Zambelli, G.M. Prazzoli, G.Pesole, G.Pavesi
Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets.
Nucleic Acids Research 2012 40(Web Server issue):W510-W515.
PscanChIP: F.Zambelli, G.Pesole, G.Pavesi
PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.
Nucleic Acids Research 2013 41(Web Server issue):W535-W543.
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