I have noticed that when I blast my own database in particular some of the sequences get truncated. This is using my local blast algorithm.
For example I know that the sequence `FYNTSTPQ` and `FYNTSTRR` would align nicely like this:
FYNTSTPQ
FYNTST
FYNTSTRR
but the output for blast p will truncate them so you only see the matching amino acids in the middle
FYNTST
FYNTST
FYNTST
Does anyone know how I can get around this truncation, it is critical I know what these amino acids are that diverge from the template...
Cheers,
Jordan
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