HHfilter statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HHfilter
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Tool usage distribution map

This map represents all the scientific publications referring to HHfilter per scientific context
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Protocols

HHfilter specifications

Information


Unique identifier OMICS_34479
Name HHfilter
Interface Web user interface
Restrictions to use None
Input data A multiple sequence alignment.
Input format FASTA,CLUSTAL,A3M
Computer skills Basic
Stability Stable
Maintained Yes

HHfilter citations

 (18)
library_books

Impact of selected amino acids of HP0377 (Helicobacter pylori thiol oxidoreductase) on its functioning as a CcmG (cytochrome c maturation) protein and Dsb (disulfide bond) isomerase

2018
PLoS One
PMCID: 5909903
PMID: 29677198
DOI: 10.1371/journal.pone.0195358

[…] using CLANS []. The CLANS cluster map was manually analyzed and various cut-off values and four clusters were defined. Sequences from each cluster were aligned with Clustal Omega [] and filtered with HHfilter to obtain representative sequences. The representative sequences from of all clusters were collected together and aligned with PROMALS []. The alignment of 161 sequences was subsequently refi […]

call_split

Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double ring complex with unique inner cavity properties

2017
PMCID: 5777263
PMID: 29183996
DOI: 10.1074/jbc.M117.815258
call_split See protocol

[…] ch iteration, sequences to be included for the next iteration were manually reviewed. The sequences resulting from each of the searches were filtered down to a pairwise sequence identity of 90% using HHfilter in the MPI Bioinformatics Toolkit (). The sequences in these reduced sets were next clustered by their all-against-all pairwise BLAST p values in CLANS () to identify and remove incomplete or […]

library_books

Hepatitis B virus (HBV) X gene mutations and their association with liver disease progression in HBV infected patients

2017
Oncotarget
PMCID: 5739625
PMID: 29285238
DOI: 10.18632/oncotarget.22428

[…] d using MAFFT []. Sequences with N- or C-terminal overhangs were removed and a final set of 5853 sequences were realigned. The alignment was filtered for the most diverse sequences (using the program hhfilter available from the hhsearch package []. Secondary structure prediction was performed using the PsiPred server [].To predict the three dimensional (3D) structure of the HBx protein, the amino […]

library_books

Cryo EM structure of the protein conducting ERAD channel Hrd1 in complex with Hrd3

2017
Nature
PMCID: 5736104
PMID: 28682307
DOI: 10.1038/nature23314

[…] ∞) and run against the clustered UniProt database from 2016 and the fungal database from JGI to generate a multiple sequence alignment. The alignment was then filtered for redundancy and coverage (HHfilter -cov 75 -id 90). In addition, TM helices were oriented in such a way that the exposure of polar residues to the hydrophobic environment of the lipid bilayer was minimized. The identity and re […]

library_books

The Architecture of the Anbu Complex Reflects an Evolutionary Intermediate at the Origin of the Proteasome System

2017
PMCID: 5666114
PMID: 28479063
DOI: 10.1016/j.str.2017.04.005

[…] ch iteration, sequences to be included for the next iteration were manually reviewed. The sequences resulting from each of the searches were filtered down to a pairwise sequence identity of 90% using HHfilter in the MPI Bioinformatics Toolkit (). The sequences in these reduced sets were next clustered by their all-against-all pairwise BLAST P-values in CLANS (), to identify and remove incomplete o […]

library_books

Comprehensive classification of the PIN domain like superfamily

2017
Nucleic Acids Res
PMCID: 5499597
PMID: 28575517
DOI: 10.1093/nar/gkx494

[…] predicted with HHblits-improved PSIPRED () or, in case of groups that include proteins with known tertiary structures, derived from DSSP () for respective PDB files. Next, each MSA was filtered with hhfilter (‘hhfilter -cov 70 -id 90’) and used as an input to build a profile HMM with ‘hhmake’. The profiles were compared with ‘hhsearch’ () and the resulting cluster map was visualized with Cytoscap […]


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HHfilter institution(s)
Max Planck Institute for Developmental Biology, Tübingen, Germany

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