jackhmmer protocols

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jackhmmer specifications

Information


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

Maintainer


  • person_outline Sean Eddy <>

Publications for jackhmmer

jackhmmer in pipelines

 (8)
2018
PMCID: 5861437
PMID: 29471489
DOI: 10.1093/nar/gky107

[…] representations were prepared using the pymol molecular graphics system (version 1.2r3pre, schrödinger, llc) ()., homologs of h.cgli were collected from uniprotkb () by running three iterations of jackhmmer () search with the h.cgli region (237–632), covering z1 and c-terminal domains as the query. full-length sequences of all the identified homologs (e-value ≤ 10−3) were clustered at 90% […]

2016
PMCID: 4894950
PMID: 27225796
DOI: 10.1038/ncomms11659

[…] and pfmahrp1: low complexity amino-acid regions of pfsbp1 and pfmahrp1 were removed with the seg algorithm, using the following parameter: window=12; lowcut=2.3 and highcut=2.5. subsequently, a jackhmmer search was conducted against the annotated protein sets of p. falciparum (3d7), p. vivax (sal-1), p. knowlesi (h), plasmodium cynomolgi (b), plasmodium chabaudi (as), plasmodium yoelii […]

2015
PMCID: 4379102
PMID: 25821953
DOI: 10.1371/journal.pone.0118683

[…] host-pathogen interactions., hhpred [] was used to search against the cdd domain database and the pdb for distant homologues of lpg0393. close relatives of lpg0393 were found in other species using jackhmmer and the uniref100 database. duplicates from different strains of l. pneumophila were removed. a maximally non-redundant set of eight vps9 domain sequences was obtained […]

2015
PMCID: 4432964
PMID: 25924720
DOI: 10.1186/s13059-015-0655-8

[…] not considered further., evolutionary information was inferred from phylogenetic trees constructed from multiple sequence alignment of domain family seed sequences and homologous sequences from a jackhmmer search []. a non-redundant set of sequences of 90% identity or less was aligned with mafft [] with default settings. alignments were visualised with belvu [] and phylogenetic trees […]

2015
PMCID: 4494053
PMID: 26100409
DOI: 10.1093/gbe/evv091

[…] therefore, we built custom hmms for all trp subfamilies other than trp-pkd. starting with the transmembrane regions from one member of each trp subfamily from swiss-prot, we performed an iterative jackhmmer scan (). trp sequences, including 25 amino acid windows flanking the trp domain region c- and n-terminally, were aligned using muscle () and subfamilies were predicted with sci-phy (). […]


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jackhmmer in publications

 (131)
PMCID: 5906684
PMID: 29670199
DOI: 10.1038/s41598-018-24467-z

[…] if this structural relationship to znrs also extends to sequence similarity, we initiated iterative sequence similarity searches with s. solfataricus cren7 (pdb: 3kxt_a) using the psi-blast and the jackhmmer programs. interestingly, these searches recovered multiple orthologous sequences from crenarchaeota and bathyarchaeota that contained two to four cysteine residues at positions […]

PMCID: 5852022
PMID: 29540682
DOI: 10.1038/s41467-018-03477-5

[…] of 2 fs. the mds were analyzed using gromacs tools, mdanalysis and locally written python and perl scripts., homologous sequences were identified in the uniprotkb database, using eight iterations of jackhmmer, with the default search parameters. this identified 5564 non-identical baca sequences. for the previous study that applied co-evolution constraints to fold the baca structure with rosetta, […]

PMCID: 5847659
PMID: 29263101
DOI: 10.1128/JB.00681-17

[…] the current analysis revealed many rr sequences in which halx domains did not appear in the standard cdd or pfam/interpro outputs but could be recognized in iterative searches with psi-blast or jackhmmer. accordingly, several additional sequences of the halx domain (table s4a) were submitted to pfam, which should result in better recognition of this common haloarchaeal domain., some archaea […]

PMCID: 5862659
PMID: 29198957
DOI: 10.1016/j.jmb.2017.11.014

[…] aep families , we performed iterative searches (seven iterations) seeded with the aep domain of polptn2 as well as with the representative members of each of the established aep families using jackhmmer . in addition, the data set was supplemented with several aep groups, representing the recently published tthprimpol , human primpol , and primpol from the nrs-1 phage . the data set […]

PMCID: 5851651
PMID: 29499035
DOI: 10.1371/journal.pcbi.1005983

[…] that the area does not contain further nondominated points. the search procedure is carried out until the complete search space has been explored., multiple sequence alignments (msa), created by jackhmmer[], were used for the inference of the maximum entropy models of the factor viii c2-domain (residues 2,188–2,345 of fa8_human, supplementary ). to optimize residue coverage and msa […]


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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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