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need help--Perl to extract encoding DNA

Asked by CRAZYCRAZY in Miscellaneous Programming, Perl Programming Language

Tags: programming, perl, bioinformatics

Hi everyone, I am new here. I wanner use perl to extract the encoding part of DNA. Our input will be a protein sequence and a DNA sequence. The protein sequence is encoded in the DNA sequence. For example: a protein sequence FICEDDPKQR is encoded in the
() part of the DNA sequence
ATGAAAATT(TTCATTTGCGAAGACGATCCAAAACAAAGA)GAAAACATGGTTACC
I wanner use Perl to extract the encoding part and save it into a new DNA sequence file.

Since the reverse translation of protein to DNA is a little complicated, I am wondering to translate our dna sequence in 3 reading frames to 3 new different protein sequences(I can write this script), then match with the input protein sequence. If match, then reverse the new match protein sequence to DNA sequence and extract it.
[+][-]11/06/09 11:57 AM, ID: 25762489Expert Comment

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[+][-]11/08/09 11:09 AM, ID: 25771450Expert Comment

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[+][-]11/08/09 06:11 PM, ID: 25773017Author Comment

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[+][-]11/23/09 08:58 AM, ID: 25889316Expert Comment

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