Hello all! I have a list of pairs of proteins and I want to compare speed and accuracy of "BLAST Two Sequences" to a Smith-Waterman program for alignment. I know there is a "Blast Two Sequences" option on NCBI website, but I would like to run it from a python script. Perhaps Biopython has this capability? If I cannot use Blast Two Sequences, I will compare different versions of Smith-Waterman, but this would not be nearly as exciting :) OR, if anyone has another idea for a great senior year project in Bioinformatics involving comparing pairs of proteins, please don't hesitate to let me know！ Thank you in advance.
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