Entering edit mode
12.7 years ago
User 2398
•
0
hi BioStar people,
I am a bioinformatics newbie, so please excuse my (probably) ignorant question.
How can one identify AA unique to one species/variant?
The input would be a FASTA or an MSA (e.g. Clustal or Muscle alignment):
VariantA
MPSG
VariantB
MESG
VariantC
MPSG
output => Report that P>E is unique to Variant B.
Thankyou for you help. I hope I can contribute to this forum once I get my feet wet in the field. Any scripts/tools to achieve the above goal would be very much appreciated.
Fz
What size data set are you dealing with? Can you not look at your data, as with your example, and determine which variant is unique?
The data set contains a few thousand peptide sequences. It could be done by hand, but would be very painful.
This also means all your peptide sequences are of equal length. Correct me if I am wrong. Of course I mean in the FASTA sequences. They are of same length in the alignment anyways. Also give me the exact input format - whether it is a alignment of multi fasta format or what..? Post 2-3 sequences here or part of an alignment, so that I can design a tool and provide it to you.