[Bioperl-l] matrix from bl2seq

Giovanni Coppola gcoppola at ucla.edu
Wed Jan 4 20:32:15 EST 2006

Hi everybody,
I have a number of nucleotide sequences and I would like to check  
them for homology to each other.
I'd like to build a square matrix with the sequence names as rows and  
columns, and (as value) a measure of homology from the bl2seq output.

One way to do this could be:
1) download Blast
2) use BlastStandAlone iteratively to get all the possible combinations
3) parse with BPbl2seq
4) build the matrix with the parameter I want

I just wanted to check if this is the way to go...

Thank you very much and happy new year!

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