Hello
I am trying to genetically characterize strains of influenza virus, and after sequencing, I do my alignments CLUSTER W, and I get the phylogenetic trees for each gene.
I want to detect cites mutations (antigenic shift) on the HA epitope.
So, it be possible for any of you tell me how I can do this part?
thank you
Fuzzy matching will detect HA epitope variants easily. We did it this way in the recent work (Dalmau et al, 04/2014, AIDS). You could also use pattern matching packages, such as prosite scan. If you are not familiar with pattern recognition packages and you do not know any programing you could isolate the HA epitope alignment regions as follows: 1. Open the alignment in Word; 2. set font to courier and document size to 50% (otherwise the alignment might look disarranged); 3. search for the HA epitope (control/apple F); 4. select and delete residue columns before and after the epitope sequence (in apple you select columns holding the option key).
Here goest a ling to perl module for fuzzy string matching: http://search.cpan.org/~jhi/String-Approx-3.26/Approx.pm.
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