Machine Learning/Kaggle HIV: Difference between revisions
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*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]) | ||
*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 |
Revision as of 11:02, 30 June 2010
http://kaggle.com/hivprogression
- How to Handle DNA Sequences
- Use sequence alignment to organize sequences across rows (software)
- 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