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

Vertebrates

ENCODE (Human TFs) - [2065 motifs] (2018-03) - [local copy]
HT-Methyl-Selex (Human TFs) - [923 motifs] (2018-03) - [local copy]
HT-Selex (Human TFs) - [864 motifs] (2018-03) - [local copy]
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]
Human_TF_dimers (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]
JASPAR core redundant vertebrates - [719 motifs] (2018) - [local copy]

Non-vertebrate Metazoa

Drosophila DMMPMM - [41 motifs] (2010_11) - [local copy]
DrosophilaTFs - [61 motifs] (2015-11) - [local copy]
Database of Drosophila DNA-binding specificities (FlyFactorSurvey) - [652 motifs] (2016_06) - [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] - [7032 motifs] (2018-05) - [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]
JASPAR core redundant insects - [140 motifs] (2018) - [local copy]
JASPAR core redundant nematodes - [26 motifs] (2018) - [local copy]
JASPAR core redundant urochordates - [1 motifs] (2018) - [local copy]

Multi-organisms

RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
footprintDB all - [10898 motifs] (2018-05) - [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

Vertebrates

ENCODE (Human TFs) - [2065 motifs] (2018-03) - [local copy]
HT-Methyl-Selex (Human TFs) - [923 motifs] (2018-03) - [local copy]
HT-Selex (Human TFs) - [864 motifs] (2018-03) - [local copy]
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]
Human_TF_dimers (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]
JASPAR core redundant vertebrates - [719 motifs] (2018) - [local copy]

Non-vertebrate Metazoa

Drosophila DMMPMM - [41 motifs] (2010_11) - [local copy]
DrosophilaTFs - [61 motifs] (2015-11) - [local copy]
Database of Drosophila DNA-binding specificities (FlyFactorSurvey) - [652 motifs] (2016_06) - [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] - [7032 motifs] (2018-05) - [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]
JASPAR core redundant insects - [140 motifs] (2018) - [local copy]
JASPAR core redundant nematodes - [26 motifs] (2018) - [local copy]
JASPAR core redundant urochordates - [1 motifs] (2018) - [local copy]

Multi-organisms

RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
footprintDB all - [10898 motifs] (2018-05) - [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.