tmap protocols

View tmap computational protocol

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tmap specifications

Information


Unique identifier OMICS_07266
Name tmap
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline B. Persson <>

Publications for tmap

tmap in pipelines

 (2)
2013
PMCID: 3631397
PMID: 23610627
DOI: 10.1002/ece3.498

[…] alignments was done using genedoc software (nicholas et al. ). the prediction of transmembrane areas within the hemoglobin sequences was performed using the multiple sequence alignment and program tmap (persson and argos ), whereas a search for chloroplast transit peptides was done using web-based targetp 1.1 server: http://www.cbs.dtu.dk/services/targetp/ (emanuelsson et al. ). the secondary […]

2005
PMCID: 1276791
PMID: 16229745
DOI: 10.1186/1471-2148-5-55

[…] were estimated with the pi/mw prediction tool of the laquip proteomic team page []. to determine the set of orthologs coding proteins predicted to interact with the cell membrane, we used the tmap program, version 46 [], available in the emboss package (european molecular biology open software suite, []). correlation coefficient values were obtained with the pearson method. alignments […]


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tmap in publications

 (8)
PMCID: 5146282
PMID: 27836547
DOI: 10.1016/j.bbrc.2016.11.019

[…] the following servers: hhpred, quick2d , predictprotein , proteus 2.0 . the transmembrane (tm) helices/region prediction was performed by interrogating the following servers: polyview-2d (117–138) , tmap (115–132, 168–196, 370–398, 565–580) , tmpred (8–25, 165–194) , octopus (510–560) ., dhapat shorter constructs were obtained by pcr, either lacking of n-terminal portions (dhapatδ120, […]

PMCID: 4742603
PMID: 26866027
DOI: 10.7774/cevr.2016.5.1.75

[…] identical regions between omp2b sequences were considered as conserved areas., the location of signal peptide and transmembrane regions within the omp2b sequence were determined using signalp [] and tmap [] servers, respectively. surface accessibility, hydrophilicity and antigenicity of the omp2b protein were determined using immune epitope database (iedb) analysis resource […]

PMCID: 3631397
PMID: 23610627
DOI: 10.1002/ece3.498

[…] alignments was done using genedoc software (nicholas et al. ). the prediction of transmembrane areas within the hemoglobin sequences was performed using the multiple sequence alignment and program tmap (persson and argos ), whereas a search for chloroplast transit peptides was done using web-based targetp 1.1 server: http://www.cbs.dtu.dk/services/targetp/ (emanuelsson et al. ). the secondary […]

PMCID: 3462998
PMID: 22884620
DOI: 10.1016/j.fgb.2012.07.004

[…] region of hpr1 and delhpr25f and delhpr25r for the 5′-flanking region of hpr2. primers used are shown in ., prediction of transmembrane segments of the receptors was done using the tmhmm, tmap () and memsat3 () software tools of the biology-workbench versus 3.2 available at http://seqtool.sdsc.edu/cgi/bw.cgi#! and http://bioinf.cs.ucl.ac.uk/web_servers/, respectively. prediction […]

PMCID: 3198989
PMID: 21970442
DOI: 10.1186/1745-6150-6-48

[…] by the average %chsp from the five organisms, the result was multiplied by log2 and clustered with the multiple experiment viewer mev tm4 program [], using k-means and euclidean distance. the tmap program, version 46 [], available in the emboss package (http://www.emboss.org), was used to predict transmembranal segments in the protein sequences., for functional analysis, orthologs […]


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tmap institution(s)
European Molecular Biology Laboratory, Heidelberg, Germany

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