Yes its blastp I was talking about. Is there any other way to do it. I tried many online servers but could not aid me much.
I am using standalone BLAST, version 2.2.26 for which I have a query sequence and a locally created database. The sequences in the database share a 65 percent identity with the query.
Unlike identity I want the database to be sorted on the basis of similarity like A= (V,L,I,M) and not A=A. Hope I am making myself clear. Will really appreciate any help. Thank you in advance
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My understanding is that OP was asking for extracting similar residues (excluding identical residues) from alignment, not just their % and/or number
Yes, you are absolutely right. But if the extraction could be done in the form of some score or percentage,it would be more helpful. Besides finding out the synonymous mutation in the sequences is my objective. For example- how many residues in each sequence in the database have undergone synonymous mutation and how similar they are still from the query sequence.
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"A= (V,L,I,M) and not A=A. Hope i am making myself clear."
You're not.
Sorry for not being clear. In case of identity, the program searches for exact matches, for example- If (A) Alanine is replaced by only Alanine then it is a match otherwise not. But another case could be - if A (Alanine) gets substituted by any other hydrophobic residues ( ex-V,L,I,M) then it is also considered a match since they share similar characteristics. Is there a way to find those matches (the later case) in form of percentage?
Yes, there is. I suppose the used substitution matrix affects these numbers..
Thank you so much.
Sir, could you please clarify the significance of positive scoring matches. I searched through a bit, couldnt find anything. Would be grateful
Check these slides (7th page).
Link is not working.
should work now, http vs https :)
Thank you :)