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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 sequence random sequences
Matrix tools
convert matrix compare matrices matrix-clustering  matrix distrib matrix quality
Build control sets
random gene selection random sequence 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 consensus
Pattern matching
matrices matrix-scan
(full options)
matrix-scan (quick) crer-scan  strings dna-pattern genome-scale dna-pattern
Comparative genomics
get orthologs get orthologs-compara  footprint-discovery footprint-scan 
NGS - ChIP-seq
peak-motifs fetch-sequences from UCSC random genome fragments
Genetic variations
Variation information Retrieve variation sequences Scan variations with motifs Convert variation formats
Conversion/Utilities
Set comparisons / enrichment compare classes/clusters Stats Frequency distribution sequences convert sequence matrices convert matrix / logo background models create background convert background sequence probability features convert features compare features
Drawing
feature map XY graph
SOAP Web services
Programmatic interface to RSAT WSDL Documentation
Help & Contact
RSAT team Training material Tutorials Publications Credits Download Motif databases Data Contact mail


Jacques van Helden