[Bioperl-l] Bio::Tools::EPCR and GFF3

[Firoz Ahmed]

Dear Jason Stajich,


I am new in BioPerl. I run e-PCR version 2.3.11 on a genomic sequence, and
got a output file "seq1.epcr" by following command:


./e-PCR -w9 -f 1 -m5000 test.sts  WS240.genomic.fa N=1 G=1 T=3 >seq1.epcr


"seq1.epcr" output looks like:


I       FOR_F32H2.2     +       8966315 8966961 647/5000-5000   1       0

I       FOR_Y54E10BR.d  -       3028477 3031091 2615/5000-5000  1       0

III     FOR_B0280.1.v5  +       7133931 7135112 1182/5000-5000  2       0




Now, I want to extract the amplicon sequences in fasta format from
"WS240.genomic.fa" according to STS hits result "seq1.epcr".


However, I want amplicon sequences contains:

(1) Only exon sequence

(2) If primer hits on non-exon (intron) region, take only exon sequence and
write that "forward or reverse" primer hit the intron region.


Could you please tell me how can I use GFF3 annotation file in
Bio::Tools::EPCR to extract my amplicon sequences?

I have gone through the documentation of "Bio::Tools::EPCR", but I am
facing difficult to use it.

I would appreciate if you could kindly help me to write a code for it.


Note: I have also loaded the "GFF3 and Genomic sequence" in mysql database
using "bp_seqfeature_load.pl"


Thanks

Firoz

New York University, USA
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