mhan008

#!/usr/bin/perl -w
use strict;
use Bio::SearchIO;
my $cutoff = '0.001';
my $file = 'actin-vs-basidio.BLASTP';
my $in = Bio::SearchIO->new(-format => 'blast',
                                -file => $file);

while( my $r = $in->next_result ) {
print "Query is: ", $r->query_name, " ",

mhan008

#!/usr/bin/perl
use strict;
use warnings;

my (%expr3H, %domains, %expr20H, %genes, %supercontig, %left, %right, %length );

open(my $fh => 'Nc3H.expr.tab') || die $!;
while(<$fh>) {
  my @row = split("\t",$_);
  next if $row[0] eq 'gene_id';

mhan008

#!/usr/bin/perl
use strict;
use warnings;

my @seqnames = ("AAC35278", "AnCSMA", "AfCHSF", "AAF19257", "P30573-1");
my @seqs = ("LLIAITYYNEDKVLTARTLHGVMQNPAWQKIVVCLVFDGIDPVLATIGV-VMKKDVDGKE","AMCLVTCYSEGEEGIRTTLDSIALTPN-SHKSIVVICDGIIKVLRMMRD-TGSKRHNMAK", "ALCLVTCYSEGEEGIRTTLDSIAMTPN$

for ( my $i = 0; $i <= 4 ; $i++) {
print "Sequence name is $seqnames[$i]\n";
my @residues = split('-',$seqs[$i]);

mhan008

#!/usr/bin/perl
use warnings;
use strict;
my $seq ="AGACAAGTCGGACGTTTCATCTGAGGGTTCTTCTGCCTCCGCACTTGGTGCACATCAGACAAGGCAATCA
TGGGGGACGCTCAGATGGCAGAGTTTGGAGCAGCAGCTTCTTACCTGCGAAAGTCAGATCGAGAGCGTCT
GGAAGCACAAACCCGTCCCTTTGATATGAAAAAGGAGTGTTTTGTGCCTGATCCAGATGAAGAGTATGTA
AAAGCTTCAATCGTCAGTCGTGAAGGTGACAAAGTCACTGTACAGACTGAGAAAAGAAAGACTGTAACTG
TAAAGGAAGCTGACATTCACCCCCAGAACCCTCCAAAGTTTGATAAAATTGAAGACATGGCAATGTTCAC
CTTCCTTCATGAGCCAGCCGTGCTGTTCAACCTCAAAGAGCGCTATGCAGCATGGATGATCTATACCTAC
TCAGGACTGTTTTGTGTCACTGTCAACCCCTACAAGTGGCTGCCGGTGTACAATCAGGAGGTGGTTGTAG