RSAT - variation-scan

Scan sequences bearing variants with a list of motifs to predict which motifs may be affected by the variant.

Conceptionc, implementationi and testingt:
Jacques van Heldencit , Alejandra Medina-Riveracit , Walter Santanacit , Jeremy Delerceci


Matrix collections

A set conformed by different motifs representing binding profiles for several transcription factors will be used to scan the variants. Provide your own motifs collection or select one to be used.

Input personal collection of motifs        Format 
Input motifs as text


Upload motifs file

Select one motif collection

ArabidopsisPBM (A thaliana) (2015-11)
Athamap (A thaliana) (2015-11)
DBTBS (Bacillus Subtilis) (2015-11)
Drosophila DMMPMM (2010_11)
DrosophilaTFs (2015-11)
FlyFactorSurvey (Drosohpila DNA-binding specificities) (2016_06)
Hocomoco (Human TFs) (2015-11)
Hocomoco (Mouse TFs) (2015-11)
Homer (Human TF motifs) (2016-07)
Drosophila IDMMPMM (2010_11)
Jolma_2013 (Human TFs) (2015-11)
Jolma_2013 (Human TFs dimers) (2016-05)
Yeastract s_cerevisiae (20130918)
cisBP c_elegans (2015-05_v1.02)
cisBP s_cerevisiae (2015-06_v1.02)
cisBP drosophila (2014-10_v0.9)
cisBP human (2014-10_v0.9)
cisBP mouse (2014-10_v0.9)
Cistrome (A thaliana motifs detected by DAP-seq) (2016-06)
Epigram (Human Histone marks related motifs) (2016-06)
footprintDB all (2017-09)
footprintDB-metazoa [only metazoa DNA motifs] (2017-09)
footprintDB-plants [only plant DNA motifs] (2017-09)
hPDI (Human TFs identified by protein microarray assays) (2016-06)
JASPAR core nonredundant all (2016)
JASPAR core nonredundant fungi (2016)
JASPAR core nonredundant insects (2016)
JASPAR core nonredundant nematodes (2016)
JASPAR core nonredundant plants (2016)
JASPAR core nonredundant urochordates (2016)
JASPAR core nonredundant vertebrates (2016)
JASPAR core redundant all (2016)
JASPAR core redundant fungi (2016)
JASPAR core redundant insects (2016)
JASPAR core redundant nematodes (2016)
JASPAR core redundant plants (2016)
JASPAR core redundant urochordates (2016)
JASPAR core redundant vertebrates (2016)
RegulonDB prokaryotes (2015_08)

Background

Background model estimation method

Scanning Parameters Length of sequence around the variant 
Thresholds
Field Lower
Threshold
Upper
Threshold
Weight of predicted sites
Weight difference between variants
P-value of predicted sites
P-value ratio between variants

Output 



AMR and WS are supported by a PAPIIT-UNAM (IA206517) grant.