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


Or Dynamic selection of motifs from the available collections
(select the collection and a dropdown menu will appear to select motifs)


View matrix descriptions & download full collections

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]
cisBP a_thaliana - [309 motifs] (2015-06_v1.02) - [local copy]
Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06) - [local copy]
footprintDB-plants [only plant DNA motifs] - [1738 motifs] (2018-06) - [local copy]
JASPAR core nonredundant plants - [489 motifs] (2018) - [local copy]
JASPAR core redundant plants - [501 motifs] (2018) - [local copy]

Multi-organisms

RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
footprintDB all - [11066 motifs] (2018-06) - [local copy]
JASPAR core nonredundant all - [1404 motifs] (2018) - [local copy]
JASPAR core redundant all - [1564 motifs] (2018) - [local copy]

RNA binding

ATtRACT - [1322 motifs] (2017) - [local copy]
CISBP-RNA - [11897 motifs] (2017) - [local copy]
RBPDB - [71 motifs] (2017) - [local copy]

Select one motif collection


View matrix descriptions & download full collections

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]
cisBP a_thaliana - [309 motifs] (2015-06_v1.02) - [local copy]
Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06) - [local copy]
footprintDB-plants [only plant DNA motifs] - [1738 motifs] (2018-06) - [local copy]
JASPAR core nonredundant plants - [489 motifs] (2018) - [local copy]
JASPAR core redundant plants - [501 motifs] (2018) - [local copy]

Multi-organisms

RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
footprintDB all - [11066 motifs] (2018-06) - [local copy]
JASPAR core nonredundant all - [1404 motifs] (2018) - [local copy]
JASPAR core redundant all - [1564 motifs] (2018) - [local copy]

RNA binding

ATtRACT - [1322 motifs] (2017) - [local copy]
CISBP-RNA - [11897 motifs] (2017) - [local copy]
RBPDB - [71 motifs] (2017) - [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.