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HHsearch - inconsistent results #355
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Could it be because the HHsuite databases may only use the first 100 sequences (or some other number) in the alignment? |
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Hi,
I'm trying to use hhsearch with a customized database. Both query and database alignments represent an entire family of homologs (there is no seed sequence). Hence, I reckon that -M 50 parameter should be applied to both query and database HMMs inferred from these alignments.
I tried to apply the -M 50 parameter and then, to test if it works, I changed the order of sequences in the alignments that were used to build the query HMMs, ran hhsearch, and it seemed to be OK (the results were basically the same when compared to the results inferred from the original alignments). But then, I changed the order of sequences in the alignments that were used to build the customized database and I got different results - it seems that the -M 50 parameter does not work...
Could you please check the bash script I've been using and help me to use the tool correctly?
Thanks a lot!
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