TMHMM protocols

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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Maintainer


This tool is not maintained anymore.

Additional information


Access available upon request.

Publication for TMHMM

TMHMM IN pipelines

 (173)
2018
PMCID: 5796565
PMID: 29435100
DOI: 10.1186/s40793-017-0306-7

[…] annotation pipeline [30] was used for automated genome annotation, and functional annotations were carried out by searching against kegg [31], cog [32] and pfam [33] databases. signalp [34] and tmhmm [35] tools were used for the prediction of genes with signal peptides and transmembrane helices, respectively. searches against ncbi-nr [36], refseq [37], uniprotkb/swiss-prot [38] and tcdb […]

2018
PMCID: 5825034
PMID: 29474388
DOI: 10.1371/journal.pone.0193058

[…] purchased from mirus bio (mirus bio, madison, wi)., multiple sequence alignments were made by clustal x2 software [12] and formatted in jalview 2.9 [13]. transmembrane helices were predicted using a tmhmm server (http://www.cbs.dtu.dk/services/tmhmm)., t7 promoter sites were incorporated on either side of primers (forward, 5’-taatacgactcactatagggcggtatttacccttgtggcta-3’ and reverse, […]

2018
PMCID: 5825034
PMID: 29474388
DOI: 10.1371/journal.pone.0193058

[…] wi)., multiple sequence alignments were made by clustal x2 software [12] and formatted in jalview 2.9 [13]. transmembrane helices were predicted using a tmhmm server (http://www.cbs.dtu.dk/services/tmhmm)., t7 promoter sites were incorporated on either side of primers (forward, 5’-taatacgactcactatagggcggtatttacccttgtggcta-3’ and reverse, 5’-taatacgactcactatagggtgttgtacgtatttggcggat-3’) […]

2018
PMCID: 5851621
PMID: 29538430
DOI: 10.1371/journal.pone.0194088

[…] the crispr repeats, with the crispr reconigtion tool v1.0 [86]. details of clusters of orthologs groups are shown in s5 table., a detected with pfam v.31.0 (http://pfam.xfam.org), b detected with tmhmm server v. 2.0 (http://www.cbs.dtu.dk/services/tmhmm/), one hundred and forty genomes were selected from a first dataset as representatives of the genetic diversity of the genus pseudomonas (see […]

2018
PMCID: 5851621
PMID: 29538430
DOI: 10.1371/journal.pone.0194088

[…] v1.0 [86]. details of clusters of orthologs groups are shown in s5 table., a detected with pfam v.31.0 (http://pfam.xfam.org), b detected with tmhmm server v. 2.0 (http://www.cbs.dtu.dk/services/tmhmm/), one hundred and forty genomes were selected from a first dataset as representatives of the genetic diversity of the genus pseudomonas (see methods). the phylogenetic position of svbp6 […]

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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