TMpred protocols

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TMpred specifications

Information


Unique identifier OMICS_03883
Name TMpred
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Kay Hofmann <>

Publication for TMpred

TMpred in pipelines

 (41)
2018
PMCID: 5823469
PMID: 29425245
DOI: 10.1371/journal.pntd.0006267

[…] sequences was performed using the translate tool from the expasy proteomic tools (http://web.expasy.org/translate/). the localization and length of transmembrane domains was predicted using tmpred (http://embnet.vital-it.ch/software/tmpred_form.html). the multiple sequence alignment was performed using the program multalin [] from prabi […]

2018
PMCID: 5886685
PMID: 29621331
DOI: 10.1371/journal.pone.0195556

[…] institute, cambridge, uk) with default settings. the online software of conserved domains (cd) on the ncbi website (https://www.ncbi.nlm.nih.gov/structure/cdd/wrpsb.cgi), and signalp and tmpred on the expasy website (http://www.expasy.org/) were used for prediction analyses of conserved domains, signal peptides and transmembrane helixes, respectively., through searching the cotton […]

2018
PMCID: 5915565
PMID: 29720990
DOI: 10.3389/fpls.2018.00504

[…] also a research fellow of cnpq., we thank dr. ken cline for providing laboratory facilities and critically reading the manuscript., http://www.arabidopsis.org , http://www.ch.embnet.org/software/tmpred_form.html , https://www.arabidopsis.org/portals/expression/microarray/atgenexpress.jsp , http://www.ncbi.nlm.nih.gov/genbank , http://www.phytozome.net/ , http://translatorx.co.uk/ , […]

2018
PMCID: 5915565
PMID: 29720990
DOI: 10.3389/fpls.2018.00504

[…] a new thylakoid targeted protein that is directly involved in the abiotic stress response., arabidopsis fip and ftsh sequences were obtained from tair. transmembrane domains were predicted by tmpred., data from the atgenexpress project () is part of the tair database (the arabidopsis information resource, see foot note text 1) was analyzed with the package r/bioconductor () and normalized […]

2017
PMCID: 5288566
PMID: 28168222
DOI: 10.1128/mSphere.00229-16

[…] across all orthologues is indicated in different shades of purple (residues are colored purple if they agree with at least 50% of the residues in the column). the tentative tm (as identified by tmpred and psipred) is indicated in light blue. while all orthologues share a highly significant (p ≥ 8 × 10−9) match to the preli domain (pf04707), only the coccidian parasites shown […]


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TMpred in publications

 (469)
PMCID: 5943604
PMID: 29743632
DOI: 10.1038/s41598-018-25667-3

[…] thus, ociad2 localizes primarily to early endosomes and mitochondria., to elucidate the functionally important features of the ociad2 protein, we analyzed its primary sequence using the online tool tmpred (www.ch.embnet.org/software/tmpred_form.html). the ocia domain is a 128-amino acid sequence located in the n-terminal region of the ociad proteins. the asrij ocia domain is necessary […]

PMCID: 5940776
PMID: 29740149
DOI: 10.1038/s41598-018-25677-1

[…] the membrane-spanning regions and orientations of the clathrin heavy chain (genbank accession no. np_001136443.1) and ap-1 (genbank accession no. afn25815.1) proteins were predicted using the tmpred program (https://embnet.vital-it.ch/software/tmpred_form.html). the results showed that three and one putative transmembrane helices were found in silkworm clathrin heavy chain and ap-1, […]

PMCID: 5948995
PMID: 29686091
DOI: 10.1073/pnas.1800650115

[…] cytoplasmic membrane, periplasm, outer membrane, or extracellular space. a localization score is provided for each location, with scores of 7.5 or greater considered probable localizations. the tmpred web server () was used to predict transmembrane helices in wmel cifa. tmpred scores were generated for transmembrane helices spanning from inside-to-outside (i-o) and outside-to-inside (o-i), […]

PMCID: 5927469
PMID: 29668758
DOI: 10.1371/journal.ppat.1007004

[…] assignment server (ffas, http://ffas.sanfordburnham.org [] failed to identify any known protein folds, nor were any conserved domains identified. no transmembrane domains were identified using tmpred (https://embnet.vital-it.ch/software/tmpred_form.html) []. blast and ffas analysis of csb showed that this protein did not share homology with any characterised protein. the blast analysis […]

PMCID: 5916306
PMID: 29721300
DOI: 10.1002/ece3.3976

[…] 7tm_gpcrs superfamily conserved protein domain family was identified by ncbi. additional gpcrs, in which the transmembrane regions were wrongly predicted, were included in the compilation after tmpred analyses (expasy.org; hofmann & stoffel, ) verified the presence of seven transmembrane domains. we additionally identified those gpcrs that were most abundant in the brain transcriptome […]


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