Description

Search for protein structural hits against a foldseek database of protein structures

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

pdb{:bash}

:file

Protein structure(s) in PDB, mmCIF or mmJSON format to compare against a foldseek database (also works with folder input)

*.{pdb,mmcif,mmjson}

meta_db{:bash}

:map

Groovy Map containing sample information for the foldseek db e.g. [ id:'test', single_end:false ]

db{:bash}

:directory

foldseek database from protein structures

*

Output

name:type
description
pattern

aln{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

${meta.id}.m8{:bash}

:file

Structural comparisons file output Query, Target, Identity, Alignment length, Mismatches, Gap openings, Query start, Query end, Target start, Target end, E-value, Bit score

*.{m8}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

foldseek
GPL v3

Foldseek: fast and accurate protein structure search

search.foldseek.com/search github.com/steineggerlab/foldseek 10.1038/s41587-023-01773-0
maintainer
Github user vagkaratzas
get in touch
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