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soedinglab / hh-suite

Remote protein homology detection suite.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7
GNU General Public License v3.0
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inconsistency using fragment or whole protein #341

Open twaksman001 opened 1 year ago

twaksman001 commented 1 year ago

I used HHBlits via the MPI website

If I submit whole protein sequence - 10000 matches, mostly kinase proteins, and the alignment is to a subsection of the query.

If I resubmit this subsection, <50 matches and no kinases.

Please can you explain how this happens?

Protein sequence: NPLCPYMNRGNPNLLPQQKSSTTQGDQVYAPSMPQFSMEGNRQMYPMPPPMMPPPPMMQGFQPPFPFNPMNQQQLSMLLMSSYARAMALAQLMNMQNRFQFYQPNQYSDPAINNYSSMPATLPQQPQVDLQNNLKTEMSPEQEKQGEPGEPRESELETSQQQGELQQQEEPLNSGEGQETEVSGEREEPETRDQDILEKRKMQRALDIEIERRERLQKRKAEENELERQQKEMERMLREEEEMKRQEEETKRQILEEERKEREEKEKDIKLRQEEELRFKKIEAEKKKRNQVNNKPQGTSVRRQRKQKHTKKTVTEDIIERL