TMHMM statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

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

Download


download.png

Versioning


No version available

Maintainer


This tool is not maintained anymore.

Additional information


Access available upon request.

Publications for TMHMM

TMHMM citations

 (3278)
library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] enes 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) (). […]

library_books

Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus

2018
BMC Genomics
PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] <1e-5 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 []. […]

library_books

Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno

2018
Stand Genomic Sci
PMCID: 5944118
PMID: 29774086
DOI: 10.1186/s40793-018-0317-z

[…] ation. 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 []. […]

library_books

Short genome report of cellulose producing commensal Escherichia coli 1094

2018
Stand Genomic Sci
PMCID: 5944007
PMID: 29760866
DOI: 10.1186/s40793-018-0316-0

[…] ected 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 . […]

library_books

Transcriptomic analysis of crustacean molting gland (Y organ) regulation via the mTOR signaling pathway

2018
Sci Rep
PMCID: 5943448
PMID: 29743490
DOI: 10.1038/s41598-018-25368-x

[…] al domains, cleavage sites for signal peptides were identified using TMHMM (version number: 2.0c), and SignalP (version number: 4.1) software respectively. All the outputs obtained from BLAST, HMMER, TMHMM and SignalP were used to achieve a comprehensive annotation for each contig. We used Trinotate (version number: v3.0.2) to generate a flat file report containing all annotation information for e […]

library_books

A Meloidogyne incognita effector MiISE5 suppresses programmed cell death to promote parasitism in host plant

2018
Sci Rep
PMCID: 5940819
PMID: 29740007
DOI: 10.1038/s41598-018-24999-4

[…] alP 4.1 (http://www.cbs.dtu.dk/services/SignalP/), predisi (http://www.predisi.de/) and phobius (http://phobius.binf.ku.dk/). The prediction of transmembrane and conserved domain were performed using TMHMM (http://www.cbs.dtu.dk/services/TMHMM-2.0/) and NCBI CD-Search (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi). A phylogenetic analysis of 29 secreted homologues was performed using the m […]

Citations

Looking to check out a full list of citations?

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.

TMHMM reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review TMHMM