Machine Learning/Kaggle HIV

• Competition Website: http://kaggle.com/hivprogression

• Code Repository:

    git clone git://ml-noisebridge.git.sourceforge.net/gitroot/ml-noisebridge/ml-noisebridge

• How to Handle DNA Sequences
  • Use sequence alignment to organize sequences across rows (software) (not necessary for this project so far...)
  • Letter standards for DNA and Amino Acids: http://www.dna.affrc.go.jp/misc/MPsrch/InfoIUPAC.html

• 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:
  • http://www.youtube.com/watch?v=RO8MP3wMvqg&feature=related

• HIV Protease helps cut up HIV proteins in to their right shapes once the cell starts producing them:
  • PR Wiki: http://en.wikipedia.org/wiki/HIV-1_protease
  • PR Sequence Info: http://www.bioafrica.net/proteomics/POL-PRprot.html
  • PR Drug Resistance Info: http://hivdb.stanford.edu/cgi-bin/PositionPhenoSummary.cgi

• Reverse Transcriptase takes the viral RNA and converts it into DNA to be integrated into the cell:
  • RT Wiki: http://en.wikipedia.org/wiki/Reverse_transcriptase (see HIV subsection)
  • RT Sequence Info: http://bioafrica.mrc.ac.za/proteomics/POL-RTprot.html
  • RT Drug Resistance Info: http://hivdb.stanford.edu/cgi-bin/PositionPhenoSummary.cgi