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 & download full collections

Vertebrates

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

Non-vertebrate Metazoa

Drosophila DMMPMM - [41 motifs] (2010_11) - [local copy]
DrosophilaTFs - [61 motifs] (2015-11) - [local copy]
Drosophila IDMMPMM - [39 motifs] (2010_11) - [local copy]
RSAT non-redundant insects - [350 motifs] (2017) - [local copy]
cisBP c_elegans - [1499 motifs] (2015-05_v1.02) - [local copy]
cisBP drosophila - [1427 motifs] (2014-10_v0.9) - [local copy]
footprintDB-metazoa [only metazoa DNA motifs] - [7296 motifs] (2017-12) - [local copy]
JASPAR core nonredundant insects - [133 motifs] (2018) - [local copy]
JASPAR core nonredundant nematodes - [26 motifs] (2018) - [local copy]
JASPAR core nonredundant urochordates - [1 motifs] (2018) - [local copy]

Plants

ArabidopsisPBM (A thaliana) - [108 motifs] (2015-11) - [local copy]
Athamap (A thaliana) - [84 motifs] (2015-11) - [local copy]
RSAT non-redundant plants - [306 motifs] (2017) - [local copy]
Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06) - [local copy]
footprintDB-plants [only plant DNA motifs] - [2028 motifs] (2017-12) - [local copy]
JASPAR core nonredundant plants - [489 motifs] (2018) - [local copy]

Fungi

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

Prokaryotes

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

Multi-organisms

footprintDB all - [11763 motifs] (2017-12) - [local copy]
JASPAR core nonredundant all - [1404 motifs] (2018) - [local copy]

Upload motifs file

Select one motif collection


View matrix descriptions & download full collections

Vertebrates

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

Non-vertebrate Metazoa

Drosophila DMMPMM - [41 motifs] (2010_11) - [local copy]
DrosophilaTFs - [61 motifs] (2015-11) - [local copy]
Drosophila IDMMPMM - [39 motifs] (2010_11) - [local copy]
RSAT non-redundant insects - [350 motifs] (2017) - [local copy]
cisBP c_elegans - [1499 motifs] (2015-05_v1.02) - [local copy]
cisBP drosophila - [1427 motifs] (2014-10_v0.9) - [local copy]
footprintDB-metazoa [only metazoa DNA motifs] - [7296 motifs] (2017-12) - [local copy]
JASPAR core nonredundant insects - [133 motifs] (2018) - [local copy]
JASPAR core nonredundant nematodes - [26 motifs] (2018) - [local copy]
JASPAR core nonredundant urochordates - [1 motifs] (2018) - [local copy]

Plants

ArabidopsisPBM (A thaliana) - [108 motifs] (2015-11) - [local copy]
Athamap (A thaliana) - [84 motifs] (2015-11) - [local copy]
RSAT non-redundant plants - [306 motifs] (2017) - [local copy]
Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06) - [local copy]
footprintDB-plants [only plant DNA motifs] - [2028 motifs] (2017-12) - [local copy]
JASPAR core nonredundant plants - [489 motifs] (2018) - [local copy]

Fungi

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

Prokaryotes

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

Multi-organisms

footprintDB all - [11763 motifs] (2017-12) - [local copy]
JASPAR core nonredundant all - [1404 motifs] (2018) - [local copy]

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.