Love the software, thanks. I’ve had a request from a user to enable the use of large numbers of ambiguous letters in DNA sequence. Currently, when she pastes her sequence it is detected as protein instead of DNA and tblastn is run, so no results are returned. She was able to retrieve results directly through the NCBI website. Is there a way to force and override, at run time, on the sequence detected and algorithm used?
I wasn’t able to find documentation on the algorithm used to detect DNA from protein, does that exist somewhere? Any info greatly appreciated, thanks.
Thanks for the kind words and I am sorry I couldn’t revert sooner.
Sequence type detection is a very simple function defined at line 31 in public/js/sequenceserver.blast.js. Ambiguous characters are not taken into account to guess sequence type. But maybe we missed something. Perhaps you may only want to change the threshold to call aa vs na?
To make changes to the code and instantly test the effect run SequenceServer from the command line in development mode:
$ sequenceserver -D
Otherwise SequenceServer will read the the minified and compressed JS that it ships with, ignoring the changes you make.
Simply refresh the page after you change code. And paste your sequence to test.
Let me know how this goes for you. Happy to discuss then how to carry the changes over to production mode (default).