RSAT : variation-scan

RSAT - variation-scan

Scan sequences of polymorphic variants with a list of motifs to predict transcription factor binding sites (TFBS) affected by the variations.

Conception^c, implementationⁱ and testing^t:
Jacques van Helden^cit , Alejandra Medina-Rivera^cit , Walter Santana^cit , Jeremy Delerce^ci

Information about variation-scan

Scan variant sequences with position specific scoring matrices (PSSM) and report variations that affect the binding score, in order to predict regulatory variants.

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)

Input

1 - Select a database in list:

2 - Select a collection in list:

3 - Select one or more matrix identifiers:

View matrix descriptions & download full collections

Select one motif collection

Input

1 - Select a database in list:

2 - Select a collection in list:

Input variation sequences
Variant sequences

Upload variant sequences

Background

Background model estimation method

Markov order

Organism-specific

Organism

[List of organisms]

not seeing your favorite organism in the list ? Contact us to have it installed

Sequence type

Input your own background file

Format

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 displayemail

[Sample Output]

MANUAL

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

RSAT - variation-scan

Fungi

Multi-organisms

Non-vertebrate Metazoa

Plants

Prokaryotes

RNA binding

Vertebrates