Web resources for downloading intergenic regions from many plant species?

Question

[biolab]

Hi, everyone,

I am starting to work on plant genomes. I would like to download intergenic region sequences from many plant species. Ensembl Biomart is a good site for downloading CDS sequences, however, it seems to be unable to provide intergenic sequences. Does anyone know how to download plant intergenic sequences? Any other web resources are also OK. I much appreciate your comments. THANKS a lot in advance.

Answer 1

[mark.ziemann]

Download the genome GTF file from the Ensembl FTP site. It contains positional information for genes, exons, CDS, etc. In linux, use grep -w "gene" file.gtf to extract coordinates of genes, then bedtools complement to extract the coordinates of the intergenic regions and bedtools getfasta to retrieve the sequences.

[biolab]

Hi mark.ziemann,

Thank you every much for your answer!