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BioInformatic Seminar

I want to explain algorithms for Motif Finding Discovery in sequence, structure and networks

Samira Mali

on 26 October 2012

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Transcript of BioInformatic Seminar

Samira Mali Computational Problems in Protein Translation There are 2 types elements of Gene Regulation: Transcription Factor Binding Site Motif Finding in Sequence Motif Finding in Networks Biological Information Stream Gene Expression DNA Replication
RNA Transcription
Protein Translation There are 20 amino acids in nature. 10 types are emergency
10 types are non emergency - Homogenistic Acid Oxidation Relation between Gene and protein 1857-1936 Alkaptonuria Disease - This acid is one of the rings in decomposition chain of Phenil Alanine
amino acid. - Alkaptonuria is a hereditary disease Gene is part o DNA that defines amino acid sequences in protein Each triple sequence nocleotide in DNA molecule is one code for special amino acid. There are 64 codons for 20 Amino acids types. Cis Activator: Element around a gene in DNA
Trans Activator: is located other place but has product that causes Genes active or nonactive. Transcription factor is a Trans Activator protein.
This factor is in Eukaryote.
This factor regulates expression of other genes So, If we nonactivate genes that codes this protein, we nonactivate all places this protein can sit on. This sites are Transcription Factor Binding Sites.(TFBS) So finding the same motif in multiple genes’ regulatory regions suggests a regulatory relationship amongst those genes Algorithms: Brute Force Consensus Greedy Gibbs Sampling EM Phylogenetic Footprinting 1 2 3 4 5 6 7 Network Motifs Finding with
Structured SVM 8 Supervisor: Dr. Mir Mohsen Pedram
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