[ml] Kaggle HIV update

[Tim]

hah...actually, strike that. I didn't look closely enough at the  
counts from my phone. with all the A's it's gotta be just a very  
degenerate nucleic acid sequence.

serves me right for butting in ;-)

-tim

(sent from my iPad Nano.)

On Jun 22, 2010, at 9:29 PM, Tim <timaro at gmail.com> wrote:

> those are protein sequences, not nucleic acid sequences.  they're  
> all specific amino acids, except for B, which stands for Asp OR Asn.
>
> -tim
>
> (sent from my iPad Nano.)
>
> On Jun 22, 2010, at 8:48 PM, David Faden <dfaden at gmail.com> wrote:
>
>> Ah, that makes sense. Thank you. It looks like neither set of  
>> sequences has any Us so they're both DNA?
>>
>> > table(unlist(strsplit(d0$PR.Seq, "")))
>>
>>     A     B     C     D     G     H     K     M     N     R      
>> S     T     V     W     Y
>> 97090     1 43476     4 61977     3   104   297     9  1334    59  
>> 67495     5   155   634
>>
>> > table(unlist(strsplit(d0$RT.Seq, "")))
>>
>>      A      B      C      D      G      H      K      M      N       
>> R      S      T      V      W      Y
>> 376584      5 156864      5 196008     16    435    694    235    
>> 4207    210 213708      5    465   2523
>>
>> I'm trying to take a quick look now at mapping these back to amino  
>> acids using the table you linked, just giving up for the moment if  
>> something is ambiguous or unknown.
>>
>> On Tue, Jun 22, 2010 at 7:31 PM, Mike Schachter <mike at mindmech.com>  
>> wrote:
>> I found an explanation on the forum of the Kaggle page that
>> explains what the non-standard letters mean, it linked to this:
>>
>> http://www.dna.affrc.go.jp/misc/MPsrch/InfoIUPAC.html
>>
>>    mike
>>
>>
>>
>> On Tue, Jun 22, 2010 at 5:27 PM, Mike Schachter <mike at mindmech.com>  
>> wrote:
>> Hey David,
>>
>> Unfortunately I don't think the sequences are amino acid sequences.
>>
>> For the PR sequences, most of them have a length of 297. If it's a
>> DNA sequence, then this means it codes for 99 amino acids. A quick
>> look shows that HIV-1 Protease (the protein whose sequence we're
>> dealing with in the first sequence column) has 99 amino acid pairs:
>>
>> http://www.bioafrica.net/proteomics/POL-PRprot.html
>>
>> Does that make sense? If it does, then the sequences from the data  
>> are
>> just noisy and of poor quality, and we're going to have to throw  
>> out some
>> of the noisy data before running it through a sequence aligner. I'm  
>> in the
>> process of doing this now, and will let everyone know how things  
>> are coming
>> along at the meeting.
>>
>> See everyone tonight!
>>
>>    mike
>>
>>
>>
>>
>> On Tue, Jun 22, 2010 at 8:37 AM, David Faden <dfaden at gmail.com>  
>> wrote:
>> It looks like the sequences are already coded in terms of amino  
>> acids rather than nucleotide triples? <http://www.biogem.org/Accelrys/Sequencing/symbols_amino_acids.html 
>> >
>>
>> On Mon, Jun 21, 2010 at 10:29 PM, Thomas Lotze <thomas.lotze at gmail.com 
>> > wrote:
>> I committed some python for generating base pair triplet count  
>> features, and R code for determining frequency and doing a basic  
>> GLM including the most frequent triplets.
>> (The Noisebridge machine learning sourceforge git repository is  
>> here: https://sourceforge.net/scm/?type=git&group_id=326816  To  
>> download the files, run "git clone git://ml- 
>> noisebridge.git.sourceforge.net/gitroot/ml-noisebridge/ml- 
>> noisebridge" or, better yet, ask Mike to give you read/write access  
>> to this project so you can upload code as well)
>>
>> This got me to 53.8462 MCE, 36th out of 49 teams.
>>
>> See you tomorrow night at 9 for fun with Hadoop!
>> -Thomas
>>
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