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Results tagged with bioinformatics
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user 8060
The science of collecting and analyzing complex biological data such as genetic codes using informatics.
2
votes
2
answers
389
views
Where to find the corrected BLOSUM matrices?
I was looking at this paper which talks about the miscalculations in the BLOSUM matrices and how the "wrong" BLOSUM62 matrix performs better than the corrected version. I was trying to find the correc …
- 277
4
votes
Accepted
Where to find the corrected BLOSUM matrices?
Okay, I emailed Dr. Mark Styczynsk (one of the authors) to ask about a link to the matrix. Here are the links he gave me:
http://web.mit.edu/bamel/blosum/revised_blosum.c
http://web.mit.edu/bamel/bl …
- 277
5
votes
1
answer
914
views
Blosum matrix with probabilities instead of the positive and negative scores
I am trying to find a version of the BLOSUM matrix that has the frequencies instead of the scaled log-odds. i.e. instead of the common version that tells us that the score LEU/ASP is -4, I would like …
- 277
1
vote
1
answer
208
views
Datasets of aligned nucleotide sequences [closed]
Where can I find some datasets of aligned nucleotide sequences? And what should I assume about the accuracy of the alignments there?
(I would like to use such datasets for training the alignment mode …
- 277
1
vote
1
answer
108
views
Applying Constraint Programming to sequence alignment/analysis
My Masters program is focused on formal methods such as SAT solving and constraint programming. I am interested in applying such techniques to problems in sequence alignment and sequence analysis, are …
- 277
4
votes
2
answers
194
views
where to find the relative frequency distribution of synonymous codons
Most amino acids can be encoded by more than one codon. For example, Serine can be encoded by any one of {UCU, UCC, UCA, UCG, AGU, AGC}.
My question is in two parts:
1) what are the relative frequ …
- 277