[Bioperl-l] extracting oriented subsequences

V.Kuryshev@Dkfz-Heidelberg.de V.Kuryshev@Dkfz-Heidelberg.de
Tue, 14 Aug 2001 18:06:52 +0200 (CEST)

Dear All,

I am new in this mail-list and hope that my request is in topic of interest.

I am looking for the program (script) which can help to extract from one or 
number of sequences (fasta) some subsequences using their coordinates from 
separate text file like:

ACnnnnn1  12001 13000
ACnnnnn1  14209 15787
ACnnnnn3  1009  15787
ACnnnn11  429   5787

and collect them in new fasta-file.

Important thing is that orientation of subsequences should follow the rule : 
from small number to biger (if it's written ACnnnn 456 345 it means that 
corresponded subsequence will be written in new file as reverce complement to 
original sequence)
E.g. it can be useful if you make assembling from draft(HTGS) genomic sequences 
(contain unordered pieces).  

I've just started to learn Perl for bioinformatics purposes and will be glad to  
hear any advices to improve this studing from Internet.   

Thank you in advance.


Molecular Genome Analysis
German Cancer Research Center
Im Neuenheimer Feld 506
Lab 056
D-69120 Heidelberg
Phone:  +49 6221 42 4701
Fax:    +49 6221 42 4704
e-mail: V.Kuryshev@dkfz.de