I'm looking for the global amino acid alignment functions/program that can be easily wrapped into Python. I operate on single query and set of up to a few hundred targets to align. So far I've been using BLAT. It's very fast, but both query and targets need to be saved into files, and output is again served as a file.
Do you know of any alternative solution, preferably reading from stdin/writing to stdout, that is as fast as BLAT and can be easily wrapped into Python? I don't care that much about sensitivity, but speed is very important, thus native biopython pairwise2 is too slow.
I have explored some implementations, but all required database creation, which of course I prefer to avoid.
Handling nucleotide alignments is a big pros, but not mandatory.
I'm not looking for sequence similarity search tool, but for global alignment tool/library that can be easily wrapped into Python.