TMHMM pipeline

TMHMM specifications


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


  • person_outline Anders Krogh <>

Additional information

Access available upon request.


Unique identifier OMICS_03900
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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Additional information

Access available upon request.

Publication for TMHMM

TMHMM citations

PMCID: 5952958

[…] average protein domain length. in addition, and only for the gr family, we also required that the cp members contained a minimum of 5 of the 7 transmembrane domains (defined by the software tmhmm version 2.0c; krogh et al. 2001; phobius version 1.01; käll et al. 2004). for the cp ir/iglur members, we required the presence of the two ligand-binding domains, namely, pf00060 (ligand-gated […]

PMCID: 5897391

[…] (gmlecrlks). identical and defective sequences were identified and eliminated by manual inspection in bioedit52. the candidates were analyzed with tmhmm v. 2.0 ( to confirm the presence of predicted transmembrane domains (tms). only sequences that contained a lectin domain within the extracellular domain, a tm, and a kd were considered putative […]

PMCID: 5825034

[…] 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 (, t7 promoter sites were incorporated on either side of primers (forward, 5’-taatacgactcactatagggcggtatttacccttgtggcta-3’ and reverse, […]

PMCID: 5855719

[…] sequencing data of mannitol-treated d. spiculifolius. amino acid sequences of dssweet12 and its homologs were aligned using clustalw, and transmembrane domains in dssweet12 were predicted by the tmhmm algorithm (available online: the phylogenetic tree was constructed by the neighbor-joining method using molecular evolutionary genetics analysis (mega) […]

PMCID: 5727068

[…] using sequence manipulation suite: protein isoelectric point and sequence manipulation suite: protein molecular weight (stothard, 2000). the presence of transmembrane domains was checked using tmhmm (käll and sonnhammer, 2002) and phobius (käll et al., 2004), and membrane proteins were annotated when both tools were in concordance. the search of trna encoding genes was performed using […]

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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