使用Perl查找最大的开放阅读框架

Question

我已经创建了一个程序,可以读取可以产生互补链的DNA序列,进一步转化为mRNA.但是,我必须为该DNA找到最长的开放阅读框架.我编写了一些东西,但是当它打印出来时,我得不到答案.救命？

这就是我的意思;

# Search for the longest open reading frame for this DNA.
print "\nHere is the largest ORF, from 5' to 3':\n" ;
local $_ = $RNA_seq ;
while ( / AUG /g ) {
    my $start = pos () - 2 ;
    if ( / UGA|UAA|UAG /g ) {
        my $stop = pos ;
        $gene = substr ( $_ , $start - 1 , $stop - $start + 1 ), $/ ;
        print "$gene" ;
    }
}

# The next set of commands translates the ORF found above for an amino acid seq.
print "\nThe largest reading Frame is:\t\t\t" . $protein { "gene" } . "\n" ;
sub translate {
    my ( $gene , $reading_frame ) = @_ ;
    my %protein = ();
    for ( $i = $reading_frame ; $i < length ( $gene ); $i += 3 ) {
        $codon = substr ( $gene , $i , 3 );
        $amino_acid = translate_codon( $codon );
        $protein { $amino_acid }++;
        $protein { "gene" } .= $amino_acid ;
    }
    return %protein ;
}

sub translate_codon {
if ( $_ [ 0 ] =~ / GC[AGCU] /i )             { return A;} # Alanine;
if ( $_ [ 0 ] =~ / UGC|UGU /i )              { return C;} # Cysteine
if ( $_ [ 0 ] =~ / GAC|GAU /i )              { return D;} # Aspartic Acid;
if ( $_ [ 0 ] =~ / GAA|GAG /i )              { return Q;} # Glutamine;
if ( $_ [ 0 ] =~ / UUC|UUU /i )              { return F;} # Phenylalanine;
if ( $_ [ 0 ] =~ / GG[AGCU] /i )             { return G;} # Glycine;
if ( $_ [ 0 ] =~ / CAC|CAU /i )              { return His;} # Histine (start codon);
if ( $_ [ 0 ] =~ / AU[AUC] /i )              { return I;} # Isoleucine;
if ( $_ [ 0 ] =~ / AAA|AAG /i )              { return K;} # Lysine;
if ( $_ [ 0 ] =~ / UUA|UUG|CU[AGCU] /i )     { return Leu;} # Leucine;
if ( $_ [ 0 ] =~ / AUG /i )                  { return M;} # Methionine;
if ( $_ [ 0 ] =~ / AAC|AAU /i )              { return N;} # Asparagine;
if ( $_ [ 0 ] =~ / CC[AGCU] /i )             { return P;} # Proline;
if ( $_ [ 0 ] =~ / CAA|CAG /i )              { return G;} # Glutamine;
if ( $_ [ 0 ] =~ / AGA|AGG|CG[AGCU] /i )     { return R;} # Arginine;
if ( $_ [ 0 ] =~ / AGC|AGU|UC[AGCU] /i )     { return S;} # Serine;
if ( $_ [ 0 ] =~ / AC[AGCU] /i )             { return T;} # Threonine;
if ( $_ [ 0 ] =~ / GU[AGCU] /i )             { return V;} # Valine;
if ( $_ [ 0 ] =~ / UGG /i )                  { return W;} # Tryptophan;
if ( $_ [ 0 ] =~ / UAC|UAU /i )              { return Y;} # Tyrosine;
if ( $_ [ 0 ] =~ / UAA|UGA|UAG /i )          { return "***" ;} # Stop Codons;
}

我错过了什么吗？

Answer 1

放

use strict;
use warnings;

在代码的开头:它将有助于检测问题

一般用

return A;

如果要返回字符串,则不返回字符串而是返回文件句柄

return 'A';