RSAT - Retrieve Sequence

RSAT - Retrieve Sequence retrieves upstream or downstream sequences from lists of genes to support extraction of regulatory sequences for cis-regulatory element analysis and regulatory genomics studies.

Key Features:

• Motif discovery and scanning: Facilitates motif discovery from ChIP-seq and ATAC-seq datasets and scans sequences to locate known motifs.
• Motif analysis: Assesses motif quality, performs motif comparison, and clusters similar motifs.
• Regulatory variations analysis: Provides retrieve-variation-seq, variation-scan, and convert-variations to retrieve, scan, and convert regulatory variation data.
• Comparative genomics: Enables extraction of sequences from coordinate lists (retrieve-seq-bed), selection of motifs from motif collections (retrieve-matrix), and extraction of orthologs using get-orthologs-compara with Ensembl Compara.
• Sequence retrieval: Extracts upstream or downstream sequences starting from a list of genes.
• Pattern representation: Supports simple string-based and matrix descriptions for regulatory patterns.

Scientific Applications:

• Yeast regulatory analysis: Applicable to analysis of regulatory sequences in yeast.
• Genome-wide studies: Supports motif discovery and analysis from genome-wide datasets including ChIP-seq and ATAC-seq.
• Regulatory element investigation: Enables investigation of unknown regulatory patterns in co-regulated gene sets and identification of genes potentially regulated by known transcription factors.

Methodology:

Uses simple string-based and matrix descriptions for regulatory pattern analysis, visualizes pattern positions via feature-map programs, and supports modular piping of tools.