Fig. 1.

Schematic representation of Variation-tools: This set of tools, included in the Regulatory Sequence Analysis Tools (RSAT), focuses on assessing the impact of different allelic variants on Transcription factor binding sites. A) convert-variations allows users to input their own variants and convert them to other formats (VCF, GVF and varBed, the latter is the format used in the next step), while variation-info retrieves the annotated information of Ensembl variants installed in RSAT servers. B) The tool retrieve-variation-seq retrieves the surrounding sequence of variants (including possible haplotypes) and generates a text file with one line per allele and per variant or haplotype (varSeq format). C) Users can input their variants in varSeq format and a collection of motifs (direct input by the user or selected from RSAT available collections) to variation-scan; the tool then scans the corresponding sequences with all motifs and perform pairwise comparisons between the binding scores of each transcription factor onto all alleles of a variant or haplotype.