Download Applying AI to Human Genome

Applying AI to Human Genome
Part 1 : Collecting data
Prof. M. Embrechts
Robert Bress
Bram Heyns
Overview
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Basics of DNA
Collecting the data
Collection : my application
Perl
Goal
Basics of DNA
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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
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Human : 23 chromosomes
Chromosomes
thousands of genes
Gene
info : exons , comments : introns
Exons and introns
codons
Codon
bases
Datacollection
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Human Genome Project
NCBI website : http//www.ncbi.nlm.nih.gov
Entrez-Nucleotide.htm
NCBI Sequence Viewer.htm
Datacollection
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Human Genome Project
NCBI website : http//www.ncbi.nlm.nih.gov
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
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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 : http://www.netcat.co.uk/rob/perl/win32perltut.html
Regular Expression – Pattern Matching
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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
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/[KCZ]arl^sa/
/<I>/(.*?)<\/I>/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
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Our choice : evolutionary computing
First part : identify exon part
Second part : identify splicejunctions
Third part : combine previous parts
Hope to reach +90% accuracy
Questions
?