Difference between revisions of "Foldseek"
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| + | Example Tests Illustrating use of HPC_FOLDSEEK_DB: | ||
| + | foldseek easy-search $HPC_FOLDSEEK_DIR/foldseek/example/d1asha_ $HPC_FOLDSEEK_DB/PDB/pdb aln2.m8 tmp | ||
| − | + | foldseek easy-multimersearch $HPC_FOLDSEEK_DIR/foldseek/example/1tim.pdb.gz $HPC_FOLDSEEK_DB/PDB/pdb result tmp | |
|}} | |}} | ||
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{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
| − | + | ||
|}} | |}} | ||
Revision as of 18:01, 25 August 2024
Description
Foldseek enables fast and sensitive comparisons of large protein structure sets.
Environment Modules
Run module spider foldseek to find out what environment modules are available for this application.
System Variables
- HPC_FOLDSEEK_DIR - installation directory
- HPC_FOLDSEEK_BIN - executable directory
- HPC_FOLDSEEK_DB - database directory
Additional Information
Example Tests Illustrating use of HPC_FOLDSEEK_DB:
foldseek easy-search $HPC_FOLDSEEK_DIR/foldseek/example/d1asha_ $HPC_FOLDSEEK_DB/PDB/pdb aln2.m8 tmp
foldseek easy-multimersearch $HPC_FOLDSEEK_DIR/foldseek/example/1tim.pdb.gz $HPC_FOLDSEEK_DB/PDB/pdb result tmp