[Bioperl-l] Getting sequences by ID

Yuval Itan y.itan at ucl.ac.uk
Wed Apr 5 18:00:54 EDT 2006


Hi Torsten,

I would be grateful for an advice from you regarding Bioperl, after I was 
fiddling around trying to write the Perl script for that from scratch.
I have a large fasta file of about 20,000 genes, and another file which is a 
list of about 2,000 gene IDs (no sequences), all included in the large file. 
I need to create a fasta file which will include only the genes with these 
specific 200 IDs. I was wondering if there is a method in Bioperl that will 
allow me to do the following pseudocode:

For each $ID from 200_IDs_set_file
{
	$my_seq = get_sequence_by_ID(from large_fasta_file, $ID)
	write $my_seq into file
}

Many thanks for any hint!

Yuval 



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