CS174_Lecture3(5).pdf

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Algorithms for Regulatory Motif Discovery
Xiaohui Xie
University of California, Irvine
Today’s Goals
• Enumeration-based method
• P-value
– Binomial
– Hypergeometric
• Probabilistic modeling
– Position Weight Matrix
– EM-algorithm
The Central Dogma
Transcription
Translation
DNA
RNA
Protein
Readout from the genome
Comparison of genome size
Organisms
Genomes
Haemophilus Methannococcus
influenzae
jannaschii
Saccharomyces
cerevisiae
(baker’s yeast)
Caenorhabditis
elegans
(nematode
worm)
Drosophila
Melanogaster
(fruit fly)
Mus
musculus
(laboratory
mouse)
Homo
sapiens
(man)
Genome
(MB)
Number
of genes
1.83
1709
1.66
1682
13
6241
97
18,424
180
13,500
3200
~30,000
3500
~30,000

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