cstranslate questions [v3.0.0] about hh-suite HOT 7 CLOSED

Hello,

(1) Do you want to do the cs219 files for version 3 with version 3?
What was your command? Can you paste the corresponding entry of 4jdv_L.a3m?
(2) HHblits always needed the cs219 sequences for the prefilter. HHsearch needs the cs219 sequences now too, since we have rewritten the Viterbi algorithm, it was useful to sort the hhm's by the number of their match states. That is equal to the length of their cs219 sequences (equals the length of their entries in the cs219 ffindex). Otherwise we would have to preprocess the hhm's or a3m's in hhsearch.

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yes i like to build cs219 files for v3 using v3 tools. are cs219 files from v2 and v3 cross-compatible?

i first used ffindex_build (v3) and existing a3m files (built by v2 tools) to make the corresponding _a3m.ff{data,index}, which i then used to make the v3 cs219 files using cstranslate (v3):

${HHLIB}/bin/cstranslate -A ${HHLIB}/data/cs219.lib -D ${HHLIB}/data/context_data.lib
-x 0.3 -c 4 -f -i _a3m -o _cs219 -I a3m -b

$ more 4jdv_L.a3m

4jdv_L
EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTFTLTISSLEPEDFAVYYCQQYEFFGQGTKLEIK
ss_pred
CCCEECCCCCCCCCCCCCEEEEEECCCCCCCCEEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCCCCEEEEEC
ss_conf
941650499201299995789997377932230321008999981268701556888889811153384168826899897556655314514892678859

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Oh, I see. cstranslate cannot handle secondary structure annotations.
I will look into this. Just for the calculation of the cs219 sequences you could
generate an a3m ffdatabase without these secondary structure annotations.

On a sidenote: As far as I see, you seem to have a3m's with just a single sequence. HHblits and HHsearch perform much better with multiple sequence alignments in the database. Those can be generated with hhblits. It is explained in the userguide.

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great markus. the moment i pasted the a3m file into the textbox, i also realized those a3m's i used were all just single sequences. yes MSA's will be much better for hhsuite.

okay i will remove the SS annotations and try again.
cheers,
fred

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In the recent commit, cstranslate should now work with a3m's that include secondary structure annotations.

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yes the new commit did allow me to use existing a3m files with secondary structure annotations. thank you very much.

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This issue can be closed, right?

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