1. O Log in to amazon biolinux O For mac users O ssh ubuntu@public_dns_address O For Windows users O use putty O Hostname public_dns_address O username ubuntu mkdir bioperl cd bioperl wget http://biobase.ist.unomaha.edu/~ithapa/myfile.gbk

2. BioPerl Ishwor Thapa (02/17/2012)

3. How Perl saved the human genome project http://www.bioperl.org/wiki/How_Perl_saved_hum an_genome O DATE: Early February, 1996 O LOCATION: Cambridge, England, in the conference room of the largest DNA sequencing center in Europe.Cambridge, England, in the conference room of the largest DNA sequencing center in Europe. O OCCASION: A high level meeting between the computer scientists of this center and the largest DNA sequencing center in the United States. O THE PROBLEM: Although the two centers use almost identical laboratory techniques, almost identical databases, and almost identical data analysis tools, they still can't interchange data or meaningfully compare results. O THE SOLUTION: Perl.

4. BioPerl O Students from biocomputing course at uni- bielefeld.de O http://bioperl.org/pipermail/bioperl- l/1996-September/002618.html http://bioperl.org/pipermail/bioperl- l/1996-September/002618.html O all large genome centers worldwide

5. Installing BioPerl O BioLinux comes with BioPerl O For other machines (linux, mac, windows), O http://www.bioperl.org/wiki/Main_Page

6. Programming in Perl print “Hello World!\n”; for (int $i = 0; $i < 10; $i++) { print “$i\n”; }

7. BioPerl O Two Main Classes in BioPerl Bio::SeqIO Bio::Seq

8. using Bio::SeqIO O 3 Main Methods new next_seq write_seq

9. Genbank to Fasta converter use Bio::SeqIO; $in = Bio::SeqIO->new(-file => ”myfile.gbk", -format => ’Genbank'); $out = Bio::SeqIO->new(-file => ">myfile.fasta", -format => ’Fasta'); while ( my $seq = $in->next_seq() ) { $out->write_seq($seq); }

10. Bio::Seq O 3 Main Methods new seq subseq display_id desc revcom

11. Using Bio::Seq use Bio::SeqIO; $in = Bio::SeqIO->new(-file => "myfile.gbk", -format => 'Genbank'); while ( my $seq = $in->next_seq() ) { print $seq->display_id; print $seq->desc; #print $seq->seq; #print $seq->subseq(10,20); #print $seq->revcom->seq; }

12. SeqFeatures

13. while (my $seq = $seq_io->next_seq()) { my @features = $seq->get_SeqFeatures(); foreach my $feat(@features) { if($feat->primary_tag eq "CDS") { my @pid = $feat->get_tag_values('protein_id'); my @translation = $feat- >get_tag_values('translation'); for (my $index = 0; $index < scalar @pid; $index++) { print ">$pid[$index]"."\n"; print $translation[$index]."\n"; }