Question: Extract sequences from local genome file by coordinates
0
gravatar for camelbbs
3.1 years ago by
camelbbs650
China
camelbbs650 wrote:

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

ADD COMMENTlink modified 3.1 years ago by mastal5112.0k • written 3.1 years ago by camelbbs650
1

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

Index hg19 and extract sequence string.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by venu6.1k

This should be promoted to the correct answer.

ADD REPLYlink written 3.1 years ago by Chris Fields2.1k
0
gravatar for mastal511
3.1 years ago by
mastal5112.0k
mastal5112.0k wrote:

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>

ADD COMMENTlink written 3.1 years ago by mastal5112.0k
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