Extract sequences from local genome file by coordinates
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
1 answer
Have a look through the descriptions of BioPerl modules, especially those with Seq in the name.
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>
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You can do this with Bioperl module Bio::DB::Fasta.
Index hg19 and extract sequence string.
This should be promoted to the correct answer.