RSAT : footprint-discovery

347 organisms

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Genomes and genes

supported organisms gene information infer operons get orthologs random gene selection

Sequence tools

retrieve sequence retrieve EnsEMBL seq fetch-sequences from UCSC sequences from bed/gff/vcf purge sequence convert sequences random sequences

Matrix tools

retrieve matrix convert matrix compare matrices matrix-clustering matrix distrib matrix quality

Build control sets

random gene selection random sequences random genome fragments random-motif permute-matrix random-sites implant-sites

Motif discovery

strings oligo-analysis (words) oligo-diff (words) dyad-analysis (spaced pairs) pattern assembly strings with positional biais position-analysis (words) local-word-analysis (word and spaced pairs) matrices info-gibbs

Pattern matching

matrices matrix-scan
(full options) matrix-scan (quick) crer-scan strings dna-pattern genome-scale dna-pattern

Comparative genomics

footprint-discovery footprint-scan

NGS - ChIP-seq

peak-motifs fetch-sequences from UCSC sequences from bed/gff/vcf random genome fragments

Genetic variations (Var-tools)

Retrieve variation sequences Scan variations with motifs Convert variation formats

Conversion/Utilities

Set comparisons / enrichment Stats Frequency distribution sequences convert sequences matrices convert matrix / logo background models create background convert background sequence probability features convert features compare features networks network interactions

Drawing

feature map feature map 2 XY graph

Web services

REST API

deprecated SOAP Programmatic interface to RSAT WSDL Documentation

Help & Contact

RSAT team Training material Tutorials Publications Credits Download Motif databases Data

bug/dont understand