[Bioperl-l] extracting subsequences

[Sean Davis]

As an alternative, Jim Kent and UCSC have tools for working with .nib and
twobit files (smart storage for large sequences) that are also very fast.
They have names like "twoBitToFa".

That said, I really like Bio::DB::Fasta and use it.

Sean


On 10/25/05 10:57 PM, "Jason Stajich" <jason.stajich at duke.edu> wrote:

> Bio::DB::Fasta is the best way to do this for big sequences.
> 
> -jason
> On Oct 25, 2005, at 4:48 PM, Amit Indap wrote:
> 
>> Hi,
>> 
>> I have to extract subsequences from fasta files containing entire
>> human chromosomes. For example I would like to extract bp
>> 167506667..167523040. I know how to do this using the Bio::Seq and
>> Bio::SeqIO APIs. The problem is it takes a long time to read in an
>> entire fasta file containing a chromosome. Is there a way I can speed
>> this up?
>> 
>> The bp indices are taken from BLAT-ing my sequences to the genome. I
>> could use megablast to find which contigs my sequences lie on, and
>> then read in those files rather than the whole chromosome.
>> 
>> Any suggestions would be helpful. Thanks.
>> 
>> Amit
>> --
>> Amit Indap
>> http://www.bscb.cornell.edu/Homepages/Amit_Indap/
>> 
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> 
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
> 
> 
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