CLUSTAL O(1.2.1) multiple sequence alignment gnl|hbvcds|AB014370_PreC_P-A ------------------------------------------------------------ gnl|hbvcds|AB064314_PreC_P-A ------------------------------------------------------------ gnl|hbvcds|AB014384_C_P-C ------------------------------------------------------------ gnl|hbvcds|AB014385_C_P-C ------------------------------------------------------------ gnl|hbvcds|AB048701_PreS1_P-D atggggcagaatctttccaccagcaatcctctgggattctttcccgaccatcagttggat gnl|hbvcds|AB078031_PreS1_P-D atggggcagaatctttccaccagcaaccctctgggattctttcccgaccaccagttggat gnl|hbvcds|AB030513_S_P-A ------------------------------------------------------------ gnl|hbvcds|AB064314_S_P-A ------------------------------------------------------------ gnl|hbvcds|AB194947_PreS2_P-E ------------------------------------------------------------ gnl|hbvcds|AB194948_PreS2_P-E ------------------------------------------------------------ #### #!/usr/bin/perl use strict; use warnings; my ($rna,$rnalen,$posi, $pos, $base, $dibase,$percent); my (%bases, %occur, %count); my($max_position, $sum, $tot) = 0; my @dinucleotide = qw(A C G T);#change the number of bases my $file = $ARGV[0] or die "Please provide the input file\n"; my $column = $ARGV[1]; open (X, $file) || die "Check the input $file\n"; while () { # chomp $_; if ($_=~/^#/) { next; } if ($_=~/^\s+/) { next; } if ($_=~/^CLUSTAL/) { next; } if ($_=~/\*/) { next; } my @temp = split (/\s+/, $_); $rna = $temp[$column]; $rna = uc $rna; $rnalen = length($rna); my @nucleotides = split (//,$rna); $tot++; foreach my $key(@dinucleotide) { $bases{$key}=1; $sum++; } $max_position = $rnalen if($rnalen > $max_position); for (my $position=0;$position<=$rnalen-1;$position++) { $dibase = substr($rna, $position, 1); #change the splitting number foreach my $dinucleotide(@dinucleotide) { if ($dibase eq $dinucleotide){ $posi = $position+1; $occur{$posi,$dibase}++; # print "$posi\t$dibase\n"; } } } } for($pos=1;$pos<=$max_position;$pos++) { print "$pos\t"; foreach $base(sort keys %bases) { print "$base\t"; if(exists $occur{$pos,$base}) { my $percent = sprintf ("%0.1f", (($occur{$pos,$base})/$tot)*100); # print "$occur{$pos,$base}\t"; print "$percent\t"; } else { print "0\t"; } } print "\n"; } close (X); #### 1 A 20.0 C 0 G 0 T 0 2 A 0 C 0 G 0 T 20.0 3 A 0 C 0 G 20.0 T 0 4 A 0 C 0 G 20.0 T 0 5 A 0 C 0 G 20.0 T 0 6 A 0 C 0 G 20.0 T 0 7 A 0 C 20.0 G 0 T 0 8 A 20.0 C 0 G 0 T 0 9 A 0 C 0 G 20.0 T 0 10 A 20.0 C 0 G 0 T 0 11 A 20.0 C 0 G 0 T 0 12 A 0 C 0 G 0 T 20.0 13 A 0 C 20.0 G 0 T 0 14 A 0 C 0 G 0 T 20.0 15 A 0 C 0 G 0 T 20.0 16 A 0 C 0 G 0 T 20.0 17 A 0 C 20.0 G 0 T 0 18 A 0 C 20.0 G 0 T 0 19 A 20.0 C 0 G 0 T 0 20 A 0 C 20.0 G 0 T 0 21 A 0 C 20.0 G 0 T 0 22 A 20.0 C 0 G 0 T 0 23 A 0 C 0 G 20.0 T 0 24 A 0 C 20.0 G 0 T 0 25 A 20.0 C 0 G 0 T 0 26 A 20.0 C 0 G 0 T 0 27 A 0 C 10.0 G 0 T 10.0 28 A 0 C 20.0 G 0 T 0 29 A 0 C 20.0 G 0 T 0 30 A 0 C 0 G 0 T 20.0 31 A 0 C 20.0 G 0 T 0 32 A 0 C 0 G 0 T 20.0 33 A 0 C 0 G 20.0 T 0 34 A 0 C 0 G 20.0 T 0 35 A 0 C 0 G 20.0 T 0 36 A 20.0 C 0 G 0 T 0 37 A 0 C 0 G 0 T 20.0 38 A 0 C 0 G 0 T 20.0 39 A 0 C 20.0 G 0 T 0 40 A 0 C 0 G 0 T 20.0 41 A 0 C 0 G 0 T 20.0 42 A 0 C 0 G 0 T 20.0 43 A 0 C 20.0 G 0 T 0 44 A 0 C 20.0 G 0 T 0 45 A 0 C 20.0 G 0 T 0 46 A 0 C 0 G 20.0 T 0 47 A 20.0 C 0 G 0 T 0 48 A 0 C 20.0 G 0 T 0 49 A 0 C 20.0 G 0 T 0 50 A 20.0 C 0 G 0 T 0 51 A 0 C 10.0 G 0 T 10.0 52 A 0 C 20.0 G 0 T 0 53 A 20.0 C 0 G 0 T 0 54 A 0 C 0 G 20.0 T 0 55 A 0 C 0 G 0 T 20.0 56 A 0 C 0 G 0 T 20.0 57 A 0 C 0 G 20.0 T 0 58 A 0 C 0 G 20.0 T 0 59 A 20.0 C 0 G 0 T 0 60 A 0 C 0 G 0 T 20.0 #### CLUSTAL O(1.2.1) multiple sequence alignment 1 60 gnl|hbvcds|AB014370_PreC_P-A ------------------------------------------------------------ gnl|hbvcds|AB064314_PreC_P-A ------------------------------------------------------------ gnl|hbvcds|AB014384_C_P-C ------------------------------------------------------------ gnl|hbvcds|AB014385_C_P-C ------------------------------------------------------------ gnl|hbvcds|AB048701_PreS1_P-D atggggcagaatctttccaccagcaatcctctgggattctttcccgaccatcagttggat gnl|hbvcds|AB078031_PreS1_P-D atggggcagaatctttccaccagcaaccctctgggattctttcccgaccaccagttggat gnl|hbvcds|AB030513_S_P-A ------------------------------------------------------------ gnl|hbvcds|AB064314_S_P-A ------------------------------------------------------------ gnl|hbvcds|AB194947_PreS2_P-E ------------------------------------------------------------ gnl|hbvcds|AB194948_PreS2_P-E ------------------------------------------------------------ 61 120 gnl|hbvcds|AB014370_PreC_P-A tagagtctcctgagcattgctcacctcaccatactgcactcaggcaagccattctctgct gnl|hbvcds|AB064314_PreC_P-A tagagtctcctgagcattgctcacctcaccatacggcactcaggcaagccattctctgct gnl|hbvcds|AB014384_C_P-C tagagtctccggaacattgttcacctcaccatacagcactcaggcaagctattctgtgtt gnl|hbvcds|AB014385_C_P-C tagagtctccggaacattgttcacctcaccatacagcactcaggcaagctattctgtgtt gnl|hbvcds|AB048701_PreS1_P-D gggtttttcttgttgacaagaatcctcacaataccgcagagtctagactcgtggtggact gnl|hbvcds|AB078031_PreS1_P-D gggtttttcttgttgacaagaatcctcacaataccgcagagtctagactcgtggtggact gnl|hbvcds|AB030513_S_P-A gggtttttcttgttgacaagaatcctcacaataccgcagagtctagactcgtggtggact gnl|hbvcds|AB064314_S_P-A gggtttttcttgttgacaagaatcctcacaataccgcagagtctagactcgtggtggact gnl|hbvcds|AB194947_PreS2_P-E gggtttttcttgttgacaaaaatcctcacaataccgcagagtctagactcgtggtggact gnl|hbvcds|AB194948_PreS2_P-E gggtttttcttgttgacaaaaatcctcacaataccgcagagtctagactcgtggtggact * * ** * * ****** **** *** * * * *