Question: How to implement blosum62 substitution score in a program?
0
gravatar for Neha shri
4.0 years ago by
Neha shri30
United States
Neha shri30 wrote:

Hi everyone,

 I am trying to write a program to screen protein sequences based on their amino acid substitution score.

 Initially , tried to do it by simply placing a score of 1 (at relevant substitutions) and 0 where the substitution is deleterious. Is the logic evolutionarily meaningful?

      Another thing  is , Can i use blosum substitution scores in place of the above mentioned method?  I know there is BLAST (ppos available for this). Just want to do in a different way.

                Any pointers will be appreciated.

 

ADD COMMENTlink modified 4.0 years ago by RamRS24k • written 4.0 years ago by Neha shri30

Do you really need to re-implement this, e.g. to practice? If not you could use any local or global aligner, e.g. ssearch, ggsearch. It has various substitution matrices built in, including blosum50. 

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Michael Dondrup46k

Thank you :)

 

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Neha shri30

I didn't understand what you were trying to do. Perhaps you can use global alignment (with BLOSUM62), this will give you a measure of how much two proteins are similar. You can use needle of EMBOSS for instance (there are several publicly available EMBOSS servers and you can download it) 

ADD REPLYlink written 4.0 years ago by Asaf6.5k

Initially , tried to do it by simply placing a score of 1 (at relevant substitutions) and 0 where the substitution is deleterious. Is the logic evolutionarily meaningful?

How do you know that the AA substitution is deleterious? Did you mean nucleotide substitution leading to stop-codon?

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Michael Dondrup46k

I meant , lets say a hydrophobic non polar amino acid residue in the core of a protein is replaced (substituted) by a polar one which is meant to be on the surface. That can pretty much reduce the stability .

ADD REPLYlink written 4.0 years ago by Neha shri30
1

That's arbitrary logic. You're better off implementing BLOSUM (which you are doing, and is the right way to go).

ADD REPLYlink written 4.0 years ago by RamRS24k

Thank you :)

ADD REPLYlink written 4.0 years ago by Neha shri30
1

Also, it's BLOSUM (from BLOcks SUbstitution Matrix), not blossum :)

ADD REPLYlink written 4.0 years ago by RamRS24k
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