Hi,
I want to calculate the similarities between each protein pariwise and then implement random walk to predict interactions. A paper mentions "J. Mol. Biol. (1981) 147, 195-197" to compare two peoteins, but I am afraid that may be obsolete.
I'd like to use some popular tools like BLAST/FASTA..
Is there any good toolkit that can generate such matrix? Just similarity is enough.
Example
Protein1
Protein2
Protein3
Protein1
1
0.9
0.4
Protein2
0.9
1
0.7
Protein3
0.4
0.7
1
As far as I know, BLAST can only tell the identy between two proteins, and FASTA can also tell the similairy (though I don't know why). And FASTA is more quicker, I think.
Then another problem emerges. How to use FASTA by python? the fasta35.exe(windows OS) is interactive like following.
>>fasta35 q.fasta lib.fasta>>Enter filename for results []>>output.txt>>How many scores would you like to see? [20]
...
I'd prefer that it could output the whole consequent without any stdin. And then I can mine the results via python.
...
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