[Bioperl-l] Q: batched extraction of sub-sequences and their reverse-complements ?

[Dave Messina]

Hi Wadim,

I would like to extract the batch of subsequences (as fastas),  based on
> list of
> coordinates : i.e. 1-1000, 1001-2000 , 2001-3000 etc) from given 'large
> seqence'
> (i.e. chromosome sized >10MB)


Take a look at Bio::DB::Fasta.




> and then, ideally , I would be keen to know how to
> extract the converse set - [i.e.: extract 'same' ( I mean corresponding)
> batch
> of sequences, based on list of converse coordinates  from
> reverse-complement of
> given 'large sequence'].
>

I don't totally understand this part of your question, but this may help:

http://www.bioperl.org/wiki/BioPerl_Tutorial#Converting_coordinate_systems_.28Coordinate::Pair.2C_RelSegment.29


Dave