Hi,
I want to calculate the similarities between each protein pairwise and then implement random walk to predict interactions. A paper mentions "J. Mol. Biol. (1981) 147, 195-197" to compare two proteins, 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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written
by
Zealseeker •
I would use clustalo with the following command:
clustalo -i my-in-seqs.fa -o my-out-seqs.fa -v --distmat-out=output_mat.txt
The --distmat-out will give you a pairwise distance matrix for each protein sequence that you have in your input fasta file.
Hope this helps,
Joseph
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written
by
Joseph Hughes
It's a good toolkit and now I'm learning to use it.
The distances ranging from 0,meaning the same, to 1, meaning totally different. Most distances are larger than 0.8...
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