Applying AI to Human Genome Part 1 : Collecting data Prof. M. Embrechts Robert Bress Bram Heyns.

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Presentation transcript:

Applying AI to Human Genome Part 1 : Collecting data Prof. M. Embrechts Robert Bress Bram Heyns

Overview Basics of DNA Collecting the data Collection : my application Perl Goal

Basics of DNA DNA = polymer of 4 molecules : bases or nucleotides A = Adenine, C = Cytosine, G = Guanine, T = Thymine Replication ( copying ) and translation ( reading ) => double helix : A  T, G  C ( copying ) 3 letter combination = codon RNA : U = Uracil in place of T => Transcribing Protein = polymer composed of 20 amino acids ( reading ) => more complex structure than DNA

Transition DNA RNA Protein

Intron – Exon - Splicejunction exon 200 characters  intron thousands 30,000 genes identified out of possible 100,000 Identification gene patent

Summary Human : 23 chromosomes Chromosomes thousands of genes Gene info : exons, comments : introns Exons and introns codons Codon bases

Datacollection Human Genome Project NCBI website : http// Entrez-Nucleotide.htm NCBI Sequence Viewer.htm

Datacollection Human Genome Project NCBI website : http// Entrez-Nucleotide.htm NCBI Sequence Viewer.htm

Datacollection : my application BioBrowser Download HTML ExtractLinks() Download HTML - data ExtractData() TranslateData()

Datacollection : my application BioBrowser Download HTML ExtractLinks() Download HTML - data ExtractData() TranslateData()

Perl Practical Extraction and Report Language POD – files -> web Portability Free – CPAN modules String manipilation Extremely powerfull regex-engine Glue language designed for short and simple tasks, not equal to lack of power or “serious” features Tutorial :

Regular Expression – Pattern Matching Practical Extraction and Report Language Scan through data and extract useful information m/ PATTERN / s/ PATTERN / REPLACEMENT / 1 line Perl = 100 lines C or Java Complex, but easy

Regex examples /[KCZ]arl^sa/ / /(.*?) /i $1,$2,… i, g, c, …., *, +, ? /([0-9a-zA-Z])+/ or /([\w])+/ s/us[^a-z]/them/g or s/us\W/them/g /([acc|act][ttt|ttc|att])/ TIMTOWTDT

Part 2 : Applying AI Our choice : evolutionary computing First part : identify exon part Second part : identify splicejunctions Third part : combine previous parts Hope to reach +90% accuracy

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