• Dropout: B.S. Psychology, ISU 1995 • Dropout: B.A. Philosophy, ISU 1995 • Part-time, stipend-funded hobbyist 2006-2010 • University of Nebraska, Omaha • University of Nebraska Medical Center • Dropout: B.S. Bioinformatics, UNO 2010 • http://www.bioperl.org/wiki/Jay_Hannah • Self-taught DB / web developer since 1995. • http://github.com/jhannah Tuesday, June 11, 13
(A, C, G, or T) • Fully extended, the DNA from a single cell would have a total length of almost 6 feet. • All the DNA in your cells could reach the moon ...6000 times! • 24 distinct chromosomes • Estimated 20,000-25,0000 genes http://en.wikipedia.org/wiki/Human_genome http://www.rothamsted.ac.uk/notebook/courses/guide/dnast.htm Tuesday, June 11, 13
different between humans and mice. Only 1% different from chimpazee. [1] • “We share half our genes [DNA] with the banana.” [2] • DNA is the blueprint of ALL life. You grew from a single cell to an adult human. What made you you? Why aren’t you me? Or a chimp? Or a banana tree, a whale shark, plankton, a clover or a giant redwood? • Answer: proteins. 1. Mural, R.J., et al., Science, v. 296, May 31, 2002, p. 1661. 2. May, R., Quoted in Coglan & Boyce, New Scientist 167 (July Tuesday, June 11, 13
N Asparagine Asp D Aspartic acid Cys C Cysteine Gln Q Glutamine Glu E Glutamic acid Gly G Glycine His H Histidine Ile I Isoleucine Leu L Leucine Lys K Lysine Met M Methionine Phe F Phenylalanine Pro P Proline Ser S Serine Thr T Threonine Trp W Tryptophan Tyr Y Tyrosine Val V Valine Tuesday, June 11, 13
But these text manipulation examples are just simple map-based transforms • And the example isn't even terribly relevant — is this even a coding sequence? Tuesday, June 11, 13
But these text manipulation examples are just simple map-based transforms • And the example isn't even terribly relevant — is this even a coding sequence? • LOL dashed params Tuesday, June 11, 13
entrezgene largefasta seqxml ace excel lasergene strider agave exp locuslink swiss alf fasta mbsout swissdriver asciitree fastq metafasta tab bsml flybase_chadoxml table bsml_sax game nexml tigr chadoxml gbdriver phd tigrxml chaos gbxml pir tinyseq chaosxml gcg pln ztr ctf genbank qual Seq::SeqIO:: Look at all these formats!! Guess what? All the code for dealing with all these formats is completely non-standardized and most of it was written by a graduate student who has fallen off the face of the planet. Tuesday, June 11, 13
that write_seq() method... https://metacpan.org/source/CJFIELDS/BioPerl-1.6.901/Bio/SeqIO.pm#L519 Well... let's look at the constructor... https://metacpan.org/source/CJFIELDS/BioPerl-1.6.901/Bio/SeqIO.pm#L350 Tuesday, June 11, 13
=> $gb_file); my $seq_object = $seqio_object->next_seq; for my $feat_object ($seq_object->get_SeqFeatures) { say "primary tag: ", $feat_object->primary_tag; for my $tag ($feat_object->get_all_tags) { say " tag: $tag"; for my $value ($feat_object->get_tag_values($tag)) { say " value: $value"; } } } Tuesday, June 11, 13
$gb_file); my $seq_object = $seqio_object->next_seq; for my $feat_object ($seq_object->get_SeqFeatures) { if ($feat_object->primary_tag eq "CDS") { say $feat_object->spliced_seq->seq; # e.g. 'ATTATTTTCGCTCGCTTCTCGCGCTTTTGCGT...' if ($feat_object->has_tag('gene')) { for my $val ($feat_object->get_tag_values('gene')){ say "gene: $val”; # e.g. 'NDP', from a line like '/gene="NDP"' } } } } Tuesday, June 11, 13
$seqio_object->next_seq; for my $feat_object ($seq_object->get_SeqFeatures) { if ($feat_object->primary_tag eq "CDS") { say $feat_object->spliced_seq->seq; # e.g. 'ATTATTTTCGCTCGCTTCTCGCGCTTTTGCGT...' if ($feat_object->has_tag('gene')) { for my $val ($feat_object->get_tag_values('gene')){ say "gene: $val”; # e.g. 'NDP', from a line like '/gene="NDP"' } } } } BioPerl to the rescue! Tuesday, June 11, 13
of code. It just needs some love. Okay, a lot of love. If you have the skills to contribute, please join in and help with the cleanup. Tuesday, June 11, 13
genehack
hannesfritz
axbom
addyosmani
3n
davidcarrasco
konakalab
reverentgeek
nmsamuel
rasagy
portentint
denniskardys
marcduiker
![14 >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] ATGACTTTTGATTATGACTTGTTTGTAATTGGTGCTGGTTCTGGTGGTTTGGCTGCTTCTAAACGAGCTGC TAGCTATGGCGCAAAAGTAGCGATCGCCGAAAATGATTTAGTGGGTGGAACCTGTGTCATTCGGGGTTGTG TACCCAAAAAACTCATGGTTTATGGTTCTCACTTTCCCGCTTTATTCGAGGATGCAGCAGGCTATGGTTGG](https://files.speakerdeck.com/presentations/e8393b10b5150130552a32ce4b0305c5/slide_17.jpg){kind=link}
![25 >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] ATGACTTTTGATTATGACTTGTTTGTAATTGGTGCTGGTTCTGGTGGTTTGGCTGCTTCTAAACGAGCTGC TAGCTATGGCGCAAAAGTAGCGATCGCCGAAAATGATTTAGTGGGTGGAACCTGTGTCATTCGGGGTTGTG TACCCAAAAAACTCATGGTTTATGGTTCTCACTTTCCCGCTTTATTCGAGGATGCAGCAGGCTATGGTTGG](https://files.speakerdeck.com/presentations/e8393b10b5150130552a32ce4b0305c5/slide_28.jpg){kind=link}
![36 >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] ATGACTTTTGATTATGACTTGTTTGTAATTGGTGCTGGTTCTGGTGGTTTGGCTGCTTCTAAACGAGCTGC TAGCTATGGCGCAAAAGTAGCGATCGCCGAAAATGATTTAGTGGGTGGAACCTGTGTCATTCGGGGTTGTG TACCCAAAAAACTCATGGTTTATGGTTCTCACTTTCCCGCTTTATTCGAGGATGCAGCAGGCTATGGTTGG](https://files.speakerdeck.com/presentations/e8393b10b5150130552a32ce4b0305c5/slide_43.jpg){kind=link}
![49 >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] ATGACTTTTGATTATGACTTGTTTGTAATTGGTGCTGGTTCTGGTGGTTTGGCTGCTTCTAAACGAGCTGC TAGCTATGGCGCAAAAGTAGCGATCGCCGAAAATGATTTAGTGGGTGGAACCTGTGTCATTCGGGGTTGTG TACCCAAAAAACTCATGGTTTATGGTTCTCACTTTCCCGCTTTATTCGAGGATGCAGCAGGCTATGGTTGG](https://files.speakerdeck.com/presentations/e8393b10b5150130552a32ce4b0305c5/slide_56.jpg){kind=link}
