seanome/kmerseek
View on GitHubWhat percent identity are the protein k-mers found by kmerseek?
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#11 opened on Feb 28, 2025
Pythonenhancementgood first issue
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Description
When kmerseek search reports a match, we see the raw protein k-mers and then the hp k-mers that unify them. It would also be nice to compute the % similarity of the query and match protein sequence, to help the user see if this combination could have been found using sequence similarity alone. (the hope is no! that kmerseek does something unique)
Query Name: sp|P41958|CED9_CAEEL Apoptosis regulator ced-9 OS=Caenorhabditis elegans OX=6239 GN=ced-9 PE=1 SV=1
Match Name: sp|Q9UK96|FBX10_HUMAN F-box only protein 10 OS=Homo sapiens OX=9606 GN=FBXO10 PE=1 SV=3
query: MSIGESIDGKINDWEEPGIVGVVVCGRMMFSLK (59-92)
alpha: hphhpphphphpphpphhhhhhhhphphhhphp
match: PNWPNQPDVEPESWREAAGIYILYHGNPVVSGN (57-90)
For example, if we align the above sequences:
>sp|P41958|CED9_CAEEL(59-92)
MSIGESIDGKINDWEEPGIVGVVVCGRMMFSLK
>sp|Q9UK96|FBX10_HUMAN(57-90)
PNWPNQPDVEPESWREAAGIYILYHGNPVVSGN
These have 15.15% identity (quite low!)
And just a bit of the amino acids match up:
So this would be a cool thing to add!