jackhmmer pipeline

jackhmmer specifications


Unique identifier OMICS_14458
Name jackhmmer
Interface Web user interface
Restrictions to use None
Input data A single protein sequence or a multiple sequence alignment
Output data A profile HMM
Programming languages C, Perl, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Basic
Version 2.7.3
Stability Stable
Maintained Yes


  • person_outline Sean Eddy <>

Publications for jackhmmer

jackhmmer citations

PMCID: 5501109

[…] hmmsearch hit length. both sets were filtered according to identity (see above)., furthermore, we queried orthodb (as of feb. 2017) with full-length arrestin phmms (e-value < 0) obtained with jackhmmer. orthodb is considered to be a high quality orthology database, which contains unique orthology group assignments for proteins of interest on a given taxonomic level. we restricted […]

PMCID: 4071793

[…] structure factors to 1.25 å resolution (pdb code: 3sgg) have been deposited in the protein data bank (pdb; http://www.rcsb.org, [71])., gxgyxyp family members were obtained by an iterative jackhmmer database search [72,73] with an inclusion threshold of e = 0.0001 in uniref100, a non-redundant subset of the uniprot knowledgebase [74]. they were aligned with mafft [75] and the resulting […]

jackhmmer institution(s)
HHMI Janelia Farm Research Campus, Ashburn, VA, USA
jackhmmer funding source(s)
This work was supported by the Howard Hughes Medical Institute (HHMI).

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