[BioRuby] removing primers and corresponding quality data from sequences

George Githinji georgkam at gmail.com
Fri Feb 12 08:35:32 UTC 2010

Hi All,
I have a list of sequences and corresponding quality files for the
same data. I would like to remove the primers as well as the
corresponding quality information.
The approach that i am using is proving to be dirty and buggy,

For example given:
1.A list of sequences in fasta file format
2.A list of 4 possible primer patterns. (no idea which sequence might
contain which primer)
3.A list of quality data in phred format for each sequence,

The task is to remove the possible primers from the sequences and
anything before or after the primer.
Each sequence has at least 2 combination of primes. one on the 5' and
the other on the 3' end.

Return a list of sequences with primer ends removed and the
corresponding quality data for the primers removed.

What would be a nice way to approach this problem.

PhD Student
KEMRI/Wellcome-Trust Research Program
Skype: george_g2
Blog: http://biorelated.wordpress.com/

More information about the BioRuby mailing list