Utilities / FASTA from BED


Extract DNA sequences into a fasta file based on feature coordinates.



fastaFromBed extracts sequences from a FASTA file for each of the intervals defined in a BED file. The headers in the input FASTA file must exactly match the chromosome column in the BED file.


The output is a fasta-format sequence file.


This tool uses the BEDTools package. Please cite the article:

Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841842.

Please see the BEDTools homepage for more details.