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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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Is it possible to reconstruct .a3m with .hhm #266

Closed xptree closed 3 years ago

xptree commented 3 years ago

Dear authors,

We are running a bunch of hhblits jobs for MSA. However, we are unable to store all .a3m files due to disk space limit. We found that .hhm file could be much smaller than the .a3m file. We wonder if it is possible to reconstruct .a3m with .hhm (e.g., by hhalign and/or hhsearch).

Thanks in advance!

milot-mirdita commented 3 years ago

No, the conversion to hhm loses a lot of information that cannot be recovered anymore.

You could instead use hhfilter to thin down the a3ms by removing redundant sequences, if you are that space limited.

xptree commented 3 years ago

Thanks, @milot-mirdita!