[Bioperl-l] extracting oriented subsequences
Tue, 14 Aug 2001 18:06:52 +0200 (CEST)
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
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
Phone: +49 6221 42 4701
Fax: +49 6221 42 4704