Hello all, I've been recently working with sequence alignment of proteins. I was wondering (I am still new to this field), what is the current state-of-the-art in protein sequence alignment?
Which are some of the fastest protein-protein alignment algorithms, faster than blastp?
Thank!
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Bioaln
2 answers
From the top of my head (and assuming you are looking for global aligners): muscle, EMBOSS-emma, MAFFT, clustal-omega, MEGA (?) ... likely forgetting several others as well
Do not fully agree on this: same comment/issue as with blast : it's a search tool (and even doing a worse job than blast on the alignment part)
But I do like Diamond otherwise!
Notebook example: https://www.kaggle.com/code/geraseva/diamond
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quick comment: do NOT consider blastP as a protein aligner (or any kind of aligner for that manner).
Blast is a search tool (aka sequence-google), not an alignment tool!
Why not? It works by protein sequence alignment, does it not?
It is a local aligner, but that is very different from doing, for example, a multiple sequence alignment (even if the MSA does local alignment).
apart from the reason pointed out by jrj.healey , blast is designed (and optimized) to look for similarities between an input protein and a database of proteins based on (and this is where the confusion comes from) locally aligned similarities.
Where alignment is a means for blast it is not the goal, while it is the goal of an alignment tool.
BLAST : Basic Local Alignment SEARCH TOOL
If you would do a blast2seq run (comparing 2 prots to each other) you might get away with it, but still I would not cataloge blast as an alignment tool.
Muscle, t-coffee.. I am not sure if they are fast. But they are supposed to be better. Use multiple aligners at same time: m-coffee from t-coffee development group.