TOPCONS protocols

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TOPCONS specifications

Information


Unique identifier OMICS_07262
Name TOPCONS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Operating system Unix/Linux
Programming languages C, Java, Perl
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Arne Elofsson <>

Additional information


https://github.com/ElofssonLab/TOPCONS2/

Information


Unique identifier OMICS_07262
Name TOPCONS
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Arne Elofsson <>

Additional information


https://github.com/ElofssonLab/TOPCONS2/

Publications for TOPCONS

TOPCONS in pipelines

 (7)
2018
PMCID: 5845112
PMID: 29556202
DOI: 10.3389/fphys.2018.00158

[…] with la taq dna polymerase (takara, dalian, china) by pcr using gene-specific primers (table )., the full length orco sequences were aligned by clustalx 2.1 and edited by genedoc 2.7.0 software. topcons (http://topcons.cbr.su.se/) (tsirigos et al., ) was used to identify the number and location of predicted transmembrane domains. the topology diagrams were constructed using topo2 […]

2017
PMCID: 5491111
PMID: 28662098
DOI: 10.1371/journal.pone.0179968

[…] using maximum-likelihood with a bootstrap analysis of 1,000 replicates (phyml). the final tree was edited using figtree []., the secondary structures of hvkcc and hvn(k)cc were predicted using the topcons program (http://topcons.cbr.su.se/) []. putative n-glycosylation sites were predicted using the program glycoep (http://www.imtech.res.in/raghava/glycoep/submit.html)., […]

2016
PMCID: 4706698
PMID: 26746870
DOI: 10.1186/s13104-015-1794-4

[…] we obtained against the draft d. v. virgifera genome sequences (hugh m. robertson, personal communication) using tblastn similarity search. prediction of membrane protein topology was achieved using topcons []., multiple alignments of co2 receptor protein sequences were generated using mafft (ver. 7.215) with the l-ins-i algorithm []. the maximum-likelihood phylogenetic tree was reconstructed […]

2015
PMCID: 4411677
PMID: 25853484
DOI: 10.3390/v7041804

[…] and in silico analysis of the lysis proteins and lysis cassette has been done using protein and nucleotide blast analysis [], biosequence hmmer analysis (using profile hidden markov models) [], topcons (identifying the presence of transmembrane domains) [] and expasy sib bioinformatics resource portal []., phages su503 and su552a were isolated from the aerated bioactive stage […]

2015
PMCID: 4536197
PMID: 26271038
DOI: 10.1371/journal.pone.0135184

[…] and first methionine were predicted using the package clc main workbench. the signal peptide cleavage site was determined using signalp [] and putative transmembrane helices were predicted using topcons []. searches for motifs and sequence patterns were performed by comparison with protein families databases on expasy server []. leucine-rich repeats were identified using pfam database [] […]


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TOPCONS in publications

 (137)
PMCID: 5928044
PMID: 29712912
DOI: 10.1038/s41598-018-24263-9

[…] hamp. the former is located between residues 37–180, while the latter spans residues 185–241. the two tmds are located between residues 15 to 34 and 182 to 204 (tmhmm), or 11 to 31 and 181 to 201 (topcons). while the duf2222 domain is found between the two helices, the n-terminus of the hamp domain overlaps the second transmembrane (tm) helix by 19 (tmhmm) or 16 residues (topcons) (fig. ). […]

PMCID: 5871782
PMID: 29593213
DOI: 10.1038/s41467-018-03522-3

[…] the same six tms for the m2 domain (tm 7 to tm 12), but there was discrepancy on the predicted tms of the m1 domain. taking into account the orientation of the predicted tm helices, only uniprot and topcons solutions were compatible with the well-established intracellular n-terminal and c-terminal domains of ac5. first, tm peptides mimicking right-oriented tms derived from uniprot predictions […]

PMCID: 5879104
PMID: 29632495
DOI: 10.3389/fphys.2018.00281

[…] t. gigas ca (aax16122.1) using bioedit (hall, ). the percentage sequence identity between ddca of t. squamosa and t. gigas ca was then computed. the tm and signal peptide were predicted using the topcons program (http://topcons.cbr.su.se/). the glycosylphosphatidylinositol (gpi) anchor was predicted using the predgpi predictor program (http://gpcr.biocomp.unibo.it/predgpi/pred.htm). […]

PMCID: 5852022
PMID: 29540682
DOI: 10.1038/s41467-018-03477-5

[…] was used to model the invert-state based on this sequence alignment. the topological orientation of baca within the bacterial cytoplasmic membrane was predicted using sequence-based approaches topcons and memsat-svm and the structure-based method memembed., gromacs v5.1.2 was used to perform all molecular dynamics simulations (mds). coarse grained (cg) mds with the martini 2.2 force field, […]

PMCID: 5849751
PMID: 29535329
DOI: 10.1038/s41598-018-22476-6

[…] higher. the asymmetric ez potential of schramm & degrado on lipid-accessible residues yields an accuracy of 72.8%, while the sequence-based state-of-the-art methods octopus and the meta-server topcons (both of which contain a machine learning component) predicts opm topologies for 72.1% and 74.8% of the protein chains. for β-barrel proteins, our potentials predict opm topologies for 91.7% […]


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TOPCONS institution(s)
Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; Science for Life Laboratory, Stockholm University, Solna, Sweden; Bioinformatics Infrastructure for Life Sciences (BILS), Stockholm University, Sweden
TOPCONS funding source(s)
Supported by the Swedish Research Council [VR-NT 2012–5046, VR-M 2010–3555]; Foundation for Strategic Research; Swedish Escience Research Center and BILS (Bioinformatics Infrastructure for Life Science).

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