pLM-BLAST
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labstructbioinf
Detection of remote homology by comparison of protein language model representations
Regardless of the parameters used, aligning a sequence to itself yields the best scoring alignment with a score slightly
It seems that part of mathematical operations should be done on gpu - which may speed up the whole search. This task will require to create a specific embedding loader...
Dear developers, Thanks very much for this excellent software. I encountered these redundant local alignments after postprocessing (see the figure). These alignments are several-residue shifted with each other, and i...
``` python embeddings.py start data_set_fullseq.fasta data_set_fullseq -embedder pt --gpu -bs 0 ``` When run as above, everything works fine. However, if I use the `-nproc 2` flag, the computations are...
Hello, I'm coming back to pLM-BLAST after leaving it for a while. I really like the approach and wanted to see what improvements had been been made since October 2023....
Rewrite [https://github.com/labstructbioinf/pLM-BLAST/blob/main/scripts/plot.py](url) and integrate with the current version.
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Detection of remote homology by comparison of protein language model representations