perl_program_to_find_open_reading_...

May 28th, 2015
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Perl Program to find Open Reading Frames (ORFs) in DNA sequence and then converting into protein#!/usr/bin/perluse strict;## set to 1 for lots of debugging output#use constant DEBUG => 0;## minimum size of ORF to output#use constant MINSIZE => 20;## hash to make complement sequence#my %compnuc = ( 'A' => 'T', 'T' => 'A', 'C' => 'G', 'G' => 'C', '-' => '-', ' ' => ' ', '*' => '*', '.' => '.');## hash for translating DNA#my %DNAtoAA = ( 'GCT' => 'A', 'GCC' => 'A', 'GCA' => 'A', 'GCG' => 'A', 'TGT' => 'C', 'TGC' => 'C', 'GAT' => 'D', 'GAC' => 'D', 'GAA' => 'E', 'GAG' => 'E', 'TTT' => 'F', 'TTC' => 'F', 'GGT' => 'G', 'GGC' => 'G', 'GGA' => 'G', 'GGG' => 'G', 'CAT' => 'H', 'CAC' => 'H', 'ATT' => 'I', 'ATC' => 'I', 'ATA' => 'I', 'AAA' => 'K', 'AAG' => 'K', 'TTG' => 'L', 'TTA' => 'L', 'CTT' => 'L', 'CTC' => 'L', 'CTA' => 'L', 'CTG' => 'L', 'ATG' => 'M', 'AAT' => 'N', 'AAC' => 'N', 'CCT' => 'P', 'CCC' => 'P', 'CCA' => 'P', 'CCG' => 'P', 'CAA' => 'Q', 'CAG' => 'Q', 'CGT' => 'R', 'CGC' => 'R', 'CGA' => 'R', 'CGG' => 'R', 'AGA' => 'R', 'AGG' => 'R', 'TCT' => 'S', 'TCC' => 'S', 'TCA' => 'S', 'TCG' => 'S', 'AGT' => 'S', 'AGC' => 'S', 'ACT' => 'T', 'ACC' => 'T', 'ACA' => 'T', 'ACG' => 'T', 'GTT' => 'V', 'GTC' => 'V', 'GTA' => 'V', 'GTG' => 'V', 'TGG' => 'W', 'TAT' => 'Y', 'TAC' => 'Y', 'TAA' => ':', 'TAG' => ':', 'TGA' => ':');#

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