TMHMM protocols

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TMHMM specifications

Information


Unique identifier OMICS_03900
Name TMHMM
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Anders Krogh <>

Additional information


Access available upon request.

Information


Unique identifier OMICS_03900
Name TMHMM
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A protein sequence.
Input format FASTA
Output data TMHMM gives some statistics and a list of the location of the predicted transmembrane helices and the predicted location of the intervening loop regions.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
decodeanhmm, gnuplot, ghostscript, ppmtogif

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Publications for TMHMM

TMHMM in pipelines

 (527)
2018
PMCID: 5785536
PMID: 29371626
DOI: 10.1038/s41467-017-02342-1

[…] were aligned using mafft 7.31 and positions with more than 50% of gaps were discarded. logo consensus sequences were created using weblogo 3 program. transmembrane helices were predicted using tmhmm server 2.05 on the consensus sequences. global phylogenetic tree was constructed from a global alignment using mafft 7.310. the phylogenetic inference was made using approximate maximum […]

2018
PMCID: 5796565
PMID: 29435100
DOI: 10.1186/s40793-017-0306-7

[…] genome annotation pipeline [] was used for automated genome annotation, and functional annotations were carried out by searching against kegg [], cog [] and pfam [] databases. signalp [] and tmhmm [] tools were used for the prediction of genes with signal peptides and transmembrane helices, respectively. searches against ncbi-nr [], refseq [], uniprotkb/swiss-prot [] and tcdb [] […]

2018
PMCID: 5800017
PMID: 29402222
DOI: 10.1186/s12864-018-4498-z

[…] on protein structure and function. in addition, we used tartgetp (http://www.cbs.dtu.dk/services/targetp/) [] to predict the subcellular location of the proteins encoded by the validated genes, and tmhmm (http://www.cbs.dtu.dk/services/tmhmm/) [] to predict transmembrane helices in these proteins., additional file 1: table s1. additional file 2: additional file 3: additional file 4: figure s1. […]

2018
PMCID: 5801409
PMID: 29456553
DOI: 10.3389/fgene.2018.00019

[…] in ncbi databases. the re-prediction results were manually curated and edited when needed. re-predicted sequences are available as supplementary material., transmembrane regions were predicted using tmhmm version 2.0 (). signal peptide cleavage sites were predicted using signalp software version 4.1. mitochondria targeting sequences were predicted using targetp version 1.1 (; ) and mitoprot (), […]

2018
PMCID: 5801465
PMID: 29437922
DOI: 10.1128/mBio.02287-17

[…] sulfurreducens strain pca. the transmembrane domains depicted were predicted by memsat3 (http://bioinf.cs.ucl.ac.uk; accessed march 2017) as described previously (). all models were confirmed using tmhmm 2.0 (http://www.cbs.dtu.dk [accessed march 2017]) (), and predictions were matched across prediction servers, with the exception of chlorobium tepidum, which tmhmm2.0 predicts to have seven […]


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TMHMM in publications

 (2755)
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] and for subsequent evaluation of genome coverage (). secreted proteins were predicted using signalp v4.1 (no truncation to the sequence length) (), and transmembrane helices were predicted using tmhmm v2.0 (). potential pathogenic proteins were identified using blastp against pathogen-host interaction (phi) database v4.4 (with 4,376 entries) ()., putative homologues among the nine […]

PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] and identity > 40% against the transporter protein database, downloaded from transporter classification database []. the secretomes of 14 fungi in this study were identified by signalp 4.1 and tmhmm 2.0 []. core secondary metabolite (sm) genes and clusters were initially identified using antismash. cyps genes were identified with hmmer and then named using the cytochrome p450 homepage []., […]

PMCID: 5944118
PMID: 29774086
DOI: 10.1186/s40793-018-0317-z

[…] to identify crispr-cas sequences the crisprfinder server was used []. the pfam-a v29 database was used to predict pfam domains []. transmembrane domains were predicted with the webserver based tmhmm2 program [] and signal peptides were predicted with signalp 4.1 server []., the complete genome of strain cad16t comprises one circular chromosome (6,837,296 bp) and two circular plasmids […]

PMCID: 5944007
PMID: 29760866
DOI: 10.1186/s40793-018-0316-0

[…] using blastclust with thresholds of 70% covered length and 30% sequence identity []. crispr, transmembrane helice, signalp and pfam protein families predictions were done using crisprfinder [], tmhmm server v.2.0 [], signalp 4.0 [] and pfam 29.0 [], respectively. the distribution of genes into cogs functional categories is presented in table .table 4table 5the total is based on the total […]

PMCID: 5943448
PMID: 29743490
DOI: 10.1038/s41598-018-25368-x

[…] peptides/orfs with significant hits, respectively (table ). in addition to the blast analyses, the orf sequences were analyzed to identify predicted pfam domains (hmmer/pfam), transmembrane helices (tmhmm) and signal peptide cleavage sites (signalp). all the outputs from blastx, blastp, hmmer/pfam, tmhmm, and signalp were combined into a single annotation file using trinotate (suppl. figure […]


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TMHMM institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark; Stockholm Bioinformatics Center, Department of Biochemistry, Stockholm University, Stockholm, Sweden; Center for Genomics Research Karolinska Institutet, Stockholm, Sweden
TMHMM funding source(s)
This work was supported by a grant from the Danish National Research Foundation, and by grants from the Swedish Technical Sciences Research Council and the Foundation from Strategic Research.

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