Machine Learning/Kaggle HIV: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
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 | ||
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