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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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secondary structure prediction by addss.pl #209

Open Rippei opened 4 years ago

Rippei commented 4 years ago

I installed hh-suite in linux x86_64 and have been successfully using the HHblits function.

I use uniclust30_2018_08 to generate the multiple sequence alignment file .a3m. Then use .a3m file to search homologous sequences in pdb70.

Now I would like to use addss.pl to predict the secondary structure of the query by addss.pl query.a3m

But, I am having a trouble in getting blast to work. HHpath.pm notes that it requires the old version of blast. However, I cannot find the source to download and install it in my environment.

Could you help?

milot-mirdita commented 4 years ago

the NCBI still hosts binaries for old blast here: https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/

kad-ecoli commented 4 years ago

Users have been asking this question very frequently. Maybe we should put the link to legacy psi-blast in the README.md or addss.pl file.