Lec12-motifsearch

Lec12-motifsearch - Motif Search CMSC 423 Central Dogma of...

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Motif Search CMSC 423
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substrings encode for genes , most of which encode for proteins double-stranded, linear molecule DNA = strands are complements of each other (A T; C G) each strand is string over {A,C,G,T} mRNA proteins Transcription (T U) Translation Genome “Central Dogma” of Biology
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DNA -> mRNA -> Protein TSS Gene Intron : not translated Exon : translated Upstream region TF Binding sites Transcription factor DNA polymerase DNA Finding transcription factor binding sites can tell us about the cell’s regulatory network.
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RNA Polymerase b/c it makes RNA into a polymer is an enzyme Discovered in 1960; Nobel prize for its discovery in 1959. .. oops 1959 Nobel awarded to Severo Ochoa and Arthur Kornberg for discovering what was mistakenly believed to be RNA pol. 2006 Nobel awarded to Roger Kornberg (son of Arthur) for detailed structure of RNA pol. 1960 Sam Weiss and Jared Hurwitz discover the real RNA pol. Image of transcription occurring. Each “hair” is a piece of RNA that RNA pol is growing off of the DNA.
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Transcription Factor Binding Sites RegulonDB (Feb 27, 2010) Length of E. coli K12 TF binding sites
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Transcription Factor Binding Sites RegulonDB (Feb 27, 2010)
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Transcription Factor Binding Sites RegulonDB (Feb 27, 2010) Position -10 Position -44 X-axes of plots are not to scale.
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Transcription Network 169 transcription factors (excluding sigmas) 3322 edges 1753 activation , 1369 repression , 185 b oth , 3 unknown
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Sequence Profles CCT domain, oFten Found near one end oF plant proteins. Suppose we want to search For other examples oF this domain. How can we represent the pattern implied by these sequences? One way is a Sequence Profle
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Sequence Profles (PSSM) ...
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This note was uploaded on 01/13/2012 for the course CMSC 423 taught by Professor Staff during the Fall '07 term at Maryland.

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Lec12-motifsearch - Motif Search CMSC 423 Central Dogma of...

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