有时候我们需要得到序列的反向互补序列，可以用下面的脚本来批量处理序列。

用法：

perl  fasta_Reverse_complementary.pl  -fa input.fa  -out out.fa

input.fa是输入文件，out.fa是反向互补后的序列

输入文件格式入下所示：

>bta-26a-2
GGCUGUGGCUGGAUUCAAGUAAUCCAGGAUAGGCUGUUUCCAUCUGUGAGGCCUAUUCUU
GAUUACUUGUUUCUGGAGGCAGCU
>bta-18b
CUUGUGUUAAGGUGCAUCUAGUGCAGUUAGUGAAGCAGCUCAGAAUCUACUGCCCUAAAU
GCUCCUUCUGGCACA
>bta-29a
AUGACUGAUUUCUUUUGGUGUUCAGAGUCAAUAUAAUUUUCUAGCACCAUCUGAAAUCGG
UUAU
>bta-7f-2
UGUGGGAUGAGGUAGUAGAUUGUAUAGUUUUAGGGUCAUACCCCAUCUUGGAGAUAACUA
UACAGUCUACUGUCUUUCCCACG

代码如下：

#!/usr/bin/perl -w

use strict;
use Getopt::Long;
use Config::General;
use Bio::SeqIO;
use Bio::Seq;
my $version = "1.3";

## prepare parameters #######################################################################
## -------------------------------------------------------------------------------------------
## GetOptions

my %opts;
GetOptions(\%opts,  "fa=s", "out=s","h");
if(!defined($opts{out}) || !defined($opts{fa}) ||defined($opts{h}))
{
print <<"Usage End.";
Usage
Forced parameter:
-out          outfile                        <outfile>        must be given
-fa      fasta file     <infile>      must be given
Other parameter:
-h           Help document
Usage End.
exit;
}
my $in  = Bio::SeqIO->new(-file => "$opts{fa}" , -format => 'Fasta');
open(OUT,">$opts{out}") ||die "open file $opts{out} faild.\n";

while ( my $seq = $in->next_seq() ) {
my($id,$sequence)=($seq->id,$seq->seq);
$sequence = &reverse_complement_IUPAC($sequence);
print OUT ">$id\n$sequence\n";
}
sub reverse_complement_IUPAC {
        my $dna = shift;
        
        # reverse the DNA sequence
        
        my $revcomp = reverse($dna);
        
        # complement the reversed DNA sequence
        
        $revcomp =~ tr/ABCDGHMNRSTUVWXYabcdghmnrstuvwxy/TVGHCDKNYSAABWXRtvghcdknysaabwxr/;
        return $revcomp;
}
sub reverse_complement {
        my $dna = shift;
        
        # reverse the DNA sequence
        
        my $revcomp = reverse($dna);
        
        # complement the reversed DNA sequence
        
        $revcomp =~ tr/ACGTacgt/TGCAtgca/;
        return $revcomp;
}