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PROFtmb specifications

Information


Unique identifier OMICS_16019
Name PROFtmb
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A protein sequence (raw).
Input format FASTA-like (text)
Output data A protein report.
Output format A sequence feature annotation format.
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0
Stability Stable
Source code URL https://rostlab.org/owiki/index.php/Packages
Maintained Yes

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Maintainer


  • person_outline Henry Bigelow

Publications for PROFtmb

PROFtmb citations

 (17)
library_books

Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design

2017
Front Immunol
PMCID: 5662880
PMID: 29123525
DOI: 10.3389/fimmu.2017.01382

[…] s reported. In brief, the tool uses hidden Markov model to predict transmembrane state of the input sequences and the Krogh et al. reported 97–98% prediction sensitivity ().The TMB was computed using PROFtmb tool, which is also a hidden Markov model-based prediction program (). Only TMB of G− pathogen sequences were computed because classical G+ bacteria do not contain β-barrel membrane proteins ( […]

library_books

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

2017
Comput Struct Biotechnol J
PMCID: 5312651
PMID: 28228927
DOI: 10.1016/j.csbj.2017.01.008

[…] sed on the analysis of results from various currently available predictors.The old performance analyses for the prediction of β-TM regions , showed that methods based on the Hidden Markov Model like ProfTMB , HMM-B2TMR and PRED-TMBB were the best in terms of SOV, per-residue and per-segment accuracy. Furthermore, Bagos et al. demonstrated that the consensus prediction method ConBBPred performe […]

library_books

Genome Report: Identification and Validation of Antigenic Proteins from Pajaroellobacter abortibovis Using De Novo Genome Sequence Assembly and Reverse Vaccinology

2016
PMCID: 5295582
PMID: 28040777
DOI: 10.1534/g3.116.036673

[…] The Vaxign suite of tools utilizes the PROFtmb (), a profile-based hidden Markov model-based software program to predict the number of TM helices in a bacterial protein. A maximum threshold of one TM domain is permitted for vaccine candida […]

library_books

FmvB: A Francisella tularensis Magnesium Responsive Outer Membrane Protein that Plays a Role in Virulence

2016
PLoS One
PMCID: 4981453
PMID: 27513341
DOI: 10.1371/journal.pone.0160977

[…] nds were predicted. However, for both proteins, TMBpro predicted long N-terminal unstructured regions (Fig A in ) that likely contributed to fewer predicted beta strands than were predicted by either PROFtmb or PRED-TMBB. Taken together, 6 out of 7 bioinformatics programs indicated that FmvA is a beta barrel protein and 6 out of 7 bioinformatics programs indicated that FmvB is an outer membrane-lo […]

library_books

Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

2016
BMC Genomics
PMCID: 4765031
PMID: 26911138
DOI: 10.1186/s12864-016-2456-1

[…] regions, []), ConSurf (evolutionary conservation of amino acids, []), DISULFIND (disulfide bonds, []). For disordered region predictions, PROFbval [], UCON [] and METADISORDER [] were used. Further, PROFtmb (bacterial transmembrane β-barrels, []), Metastudent (Gene Ontology terms, []), and LocTree3 (subcellular localization, []) were applied. SignalP4.1 was used for the prediction of signal pepti […]

call_split

Mosaic composition of ribA and wspB genes flanking the virB8 D4 operon in the Wolbachia supergroup B strain, wStr

2015
Arch Microbiol
PMCID: 4705124
PMID: 26400107
DOI: 10.1007/s00203-015-1154-8
call_split See protocol

[…] s et al. ). Alignments were edited by visual inspection and modified in Microsoft Word. WspB protein structure predictions were obtained using tools available at www.predictprotein.org, including the PROFtmb program (Dell et al. ) for prediction of bacterial transmembrane beta barrels (Bigelow et al. ) and per-residue prediction of up-strand, down-strand, periplasmic loop and outer loop positions […]


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PROFtmb funding source(s)
This work was supported by grant R01-LM07329-01 from the National Library of Medicine.

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