Machine Learning/Kaggle HIV

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http://kaggle.com/hivprogression
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*Competition Website: http://kaggle.com/hivprogression
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*Code Repository:
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    git clone git://ml-noisebridge.git.sourceforge.net/gitroot/ml-noisebridge/ml-noisebridge
  
 
*How to Handle DNA Sequences
 
*How to Handle DNA Sequences
**Use [http://en.wikipedia.org/wiki/Sequence_alignment sequence alignment] to organize sequences across rows ([http://en.wikipedia.org/wiki/List_of_sequence_alignment_software software])
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**Use [http://en.wikipedia.org/wiki/Sequence_alignment sequence alignment] to organize sequences across rows ([http://en.wikipedia.org/wiki/List_of_sequence_alignment_software software]) (not necessary for this project so far...)
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**Letter standards for DNA and Amino Acids: http://www.dna.affrc.go.jp/misc/MPsrch/InfoIUPAC.html
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*There are two proteins we have sequences for - HIV Protease and HIV Reverse transcriptase. A great video that describes how these work is available here:
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**http://www.youtube.com/watch?v=RO8MP3wMvqg&feature=related
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*HIV Protease helps cut up HIV proteins in to their right shapes once the cell starts producing them:
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**PR Wiki: http://en.wikipedia.org/wiki/HIV-1_protease
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**PR Sequence Info: http://www.bioafrica.net/proteomics/POL-PRprot.html
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**PR Drug Resistance Info: http://hivdb.stanford.edu/cgi-bin/PositionPhenoSummary.cgi
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*Reverse Transcriptase takes the viral RNA and converts it into DNA to be integrated into the cell:
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**RT Wiki: http://en.wikipedia.org/wiki/Reverse_transcriptase (see HIV subsection)
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**RT Sequence Info: http://bioafrica.mrc.ac.za/proteomics/POL-RTprot.html
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**RT Drug Resistance Info: http://hivdb.stanford.edu/cgi-bin/PositionPhenoSummary.cgi

Latest revision as of 11:14, 30 June 2010

  • Code Repository:
    git clone git://ml-noisebridge.git.sourceforge.net/gitroot/ml-noisebridge/ml-noisebridge




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