Machine Learning/Kaggle HIV

From Noisebridge
< Machine Learning(Difference between revisions)
Jump to: navigation, search
Line 2: Line 2:
  
 
*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 14:
 
**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:

Revision as of 11:07, 30 June 2010

http://kaggle.com/hivprogression




Personal tools