Extract sequences from local genome file by coordinates

Question

[camelbbs]

Hi all,

I want to ask if there is a bioperl module can extract sequences by coordinates (chr1:12321321-12321921) from local genome file (eg. hg19.genome.fa). We can do that using 'bedtools getfasta', but still want to know if bioperl module can do that?

Thanks, Camel

[venu]

You can do this with Bioperl module Bio::DB::Fasta.

Index hg19 and extract sequence string.

[Chris Fields]

This should be promoted to the correct answer.

Answer 1

[mastal511]

Have a look through the descriptions of BioPerl modules, especially those with Seq in the name.

http://www.bioperl.org/w/index.php?title=Category:Modules&pagefrom=Bio%3A%3ASearchIO%3A%3Aaxt#mw-pages

The PrimarySeq module can give you a subset of a sequence, so that may be able to do what you want.

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/PrimarySeq.html/a>