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



Or select a collection in list (a box will appear to select each matrix individually)

View matrix descriptions

Vertebrates

Hocomoco (Human TFs) - [771 motifs] (2017-10)
Hocomoco (Mouse TFs) - [531 motifs] (2017-10)
Homer (Human TF motifs) - [332 motifs] (2016-07)
Jolma_2013 (Human TFs) - [818 motifs] (2015-11)
Jolma_2013 (Human TFs dimers) - [664 motifs] (2016-05)
RSAT non-redundant vertebrates - [2233 motifs] (2017)
cisBP human - [1832 motifs] (2014-10_v0.9)
cisBP mouse - [1715 motifs] (2014-10_v0.9)
Epigram (Human Histone marks related motifs) - [589 motifs] (2016-06)
hPDI (Human TFs identified by protein microarray assays) - [437 motifs] (2016-06)
JASPAR core nonredundant vertebrates - [579 motifs] (2018)

Non-vertebrate Metazoa

Drosophila DMMPMM - [41 motifs] (2010_11)
DrosophilaTFs - [61 motifs] (2015-11)
Drosophila IDMMPMM - [39 motifs] (2010_11)
RSAT non-redundant insects - [350 motifs] (2017)
cisBP c_elegans - [1499 motifs] (2015-05_v1.02)
cisBP drosophila - [1427 motifs] (2014-10_v0.9)
footprintDB-metazoa [only metazoa DNA motifs] - [7122 motifs] (2017-09)
JASPAR core nonredundant insects - [133 motifs] (2018)
JASPAR core nonredundant nematodes - [26 motifs] (2018)
JASPAR core nonredundant urochordates - [1 motifs] (2018)

Plants

ArabidopsisPBM (A thaliana) - [108 motifs] (2015-11)
Athamap (A thaliana) - [84 motifs] (2015-11)
RSAT non-redundant plants - [306 motifs] (2017)
Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06)
footprintDB-plants [only plant DNA motifs] - [1784 motifs] (2017-09)
JASPAR core nonredundant plants - [489 motifs] (2018)

Fungi

Yeastract s_cerevisiae - [732 motifs] (20130918)
cisBP s_cerevisiae - [776 motifs] (2015-06_v1.02)
JASPAR core nonredundant fungi - [176 motifs] (2018)

Prokaryotes

DBTBS (Bacillus Subtilis) - [88 motifs] (2015-11)
RegulonDB prokaryotes - [93 motifs] (2015_08)

Multi-organisms

footprintDB all - [11296 motifs] (2017-09)
JASPAR core nonredundant all - [1404 motifs] (2018)


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) (2017-10)
Hocomoco (Mouse TFs) (2017-10)
Homer (Human TF motifs) (2016-07)
Drosophila IDMMPMM (2010_11)
Jolma_2013 (Human TFs) (2015-11)
Jolma_2013 (Human TFs dimers) (2016-05)
RSAT non-redundant insects (2017)
RSAT non-redundant plants (2017)
RSAT non-redundant vertebrates (2017)
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 (2018)
JASPAR core nonredundant fungi (2018)
JASPAR core nonredundant insects (2018)
JASPAR core nonredundant nematodes (2018)
JASPAR core nonredundant plants (2018)
JASPAR core nonredundant urochordates (2018)
JASPAR core nonredundant vertebrates (2018)
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.