ChemicalJames

#!/bin/perl -w
#sort sequences into two files according to 5' barcode

use strict;
use warnings;
use Bio::SeqIO;


my $file = 'trimmed_seq.fa';
my $in = Bio::SeqIO->new(-format => 'Fasta',

ChemicalJames

#!/bin/perl -w

use strict;
use warnings;
use Bio::SeqIO;

my $seqio = Bio::SeqIO->new(-format=>'fasta',-file=>'ath_sRNA1.fa');
my $adapter='CTGTAGGCACCATCAAT';

open OUT,'>trimmed_seq.fa' or die "Cannot write to a file\n";

ChemicalJames

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

use Bio::DB::Fasta;
use Bio::Seq;
use Bio::SeqIO;

my $file = 'sacharomyces_cerevisiae_S288C.fa';
my $db = Bio::DB::Fasta->new($file);

ChemicalJames

package Temperature;
use strict; use warnings;

sub f2c {
	my $f = shift;
	my $c = (5/9) * ($f - 32);
	return $c;
}
sub c2f {
	my $c = shift;

ChemicalJames

#!/usr/bin/perl -w
 use strict;
 foreach (0..8)
 {
  my $line = <>;
  print "$_ : $line";
 }

ChemicalJames

#!bin/perl
use strict;

# number of 3'UTR
open(IN, "grep -c 'three_prime' ath_chr1.gff | ") || die $!;
while(my $count = <IN>) {
open(my $outfh => "UTR.txt") || die $!;
print $outfh "$count\n";
}

ChemicalJames

#!/bin/perl
use strict;

my %seq;
$seq{'AAC35278'} = 'LLIAITYYNEDKVLTARTLHGVMQNPAWQKIVVCLVFDGIDPVLATIGV-VMKKDVDGKE';
$seq{'AnCSMA'} = 'AMCLVTCYSEGEEGIRTTLDSIALTPN-SHKSIVVICDGIIKVLRMMRD-TGSKRHNMAK';
$seq{'AfCHSF'} = 'ALCLVTCYSEGEEGIRTTLDSIAMTPN-SHKTIIVICDGIIKVLRMMRD-TGSKRHNMAK';
$seq{'AAF19527'} = 'AILLVTAYSEGELGIRTTLDSIATTPN-SHKTILVICDGIIKVLGMMKD-RGSKRHNMAK';
$seq{'P30573-1'} = 'TINLVTCYSEDEEGIRITLDSIATTPN-SHKLILVICDGIIKVLDMMSDAQGSKRHNMAK';

ChemicalJames

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