Machine Learning/Kaggle HIV: Difference between revisions
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http://kaggle.com/hivprogression | *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 | *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]) | **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...) | ||
**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: | *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 | **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: | *HIV Protease helps cut up HIV proteins in to their right shapes once the cell starts producing them: | ||
| Line 11: | Line 17: | ||
**PR Sequence Info: http://www.bioafrica.net/proteomics/POL-PRprot.html | **PR Sequence Info: http://www.bioafrica.net/proteomics/POL-PRprot.html | ||
**PR Drug Resistance Info: http://hivdb.stanford.edu/cgi-bin/PositionPhenoSummary.cgi | **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: | *Reverse Transcriptase takes the viral RNA and converts it into DNA to be integrated into the cell: | ||
Latest revision as of 11:14, 30 June 2010
- 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:
- 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