[Bioperl-l] How to parse different (fasta) files

Tim timbourine81 at gmail.com
Wed Nov 25 12:53:34 EST 2009

Hey everybody,

another question from me...if you do not mind :)

My situation is like this: I have parsed a standalone BLAST output using
SearchIO with only the hit names. Now I have a second fasta file with
the same sequences like in the BLAST database but including an alignment
(meaning "." and "-"). (There is no chance to make a BLAST database with
fasta files including the alignment, unfortunately...).
My intention is now to take the name of the hit sequences (BLAST output)
and to get the corresponding aligned sequences (fasta file incl.
alignment) and putting it in a new file.

Is anybody out there who has tried that before?

Again, I am a absolute greenhorn in using (Bio)perl. Maybe it is very
simple :D

Looking forward to get an answer of you.

All the best,

Tim Köhler
MPI for Terrestrial Microbiology
D-35043 Marburg / Germany

Email: koehlerd at mpi-marburg.mpg.de
Phone: +49 6421 178-740
Fax:   +49 6421 178-999

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