DAS-TMfilter statistics

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Citations per year

Number of citations per year for the bioinformatics software tool DAS-TMfilter
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Tool usage distribution map

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Protocols

DAS-TMfilter specifications

Information


Unique identifier OMICS_07259
Name DAS-TMfilter
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for DAS-TMfilter

DAS-TMfilter citations

 (21)
library_books

A Novel Protein Elicitor BAR11 From Saccharothrix yanglingensis Hhs.015 Improves Plant Resistance to Pathogens and Interacts With Catalases as Targets

2018
Front Microbiol
PMCID: 5900052
PMID: 29686663
DOI: 10.3389/fmicb.2018.00700

[…] d classified in the genus Saccharothrix (). According to the genome-wide sequencing results of strain Hhs.015, we analyzed its secreted protein genes using several software of SignalPv4.1, TMHMMv2.0, DAS-TMfilter, HMMTOP, Prosite Scan, PSORT and big-PI predictor and selected some of the function-unknown putative protein genes to investigate their functions after heterologous expression. According […]

library_books

Charged residues next to transmembrane regions revisited: “Positive inside rule” is complemented by the “negative inside depletion/outside enrichment rule”

2017
BMC Biol
PMCID: 5525207
PMID: 28738801
DOI: 10.1186/s12915-017-0404-4

[…] in query protein sequences [, ], and tools such as the quite reliable TMHMM (software for predicting TMHs based on a hidden Markov model), Phobius or the dense alignment surface-transmembrane filter (DAS-TMfilter) represent today’s prediction limit of TMHs’ hydrophobic cores within the protein sequence [–]. The prediction accuracy for true positives and negatives is reported to be close to 100%, a […]

library_books

Ca2+/Cation Antiporters (CaCA): Identification, Characterization and Expression Profiling in Bread Wheat (Triticum aestivum L.)

2016
Front Plant Sci
PMCID: 5124604
PMID: 27965686
DOI: 10.3389/fpls.2016.01775

[…] The trans-membrane (TM) regions in individual TaCaCA protein was predicted using five different programs- TMHMM v2.0 (http://www.cbs.dtu.dk/services/TMHMM/), TMMOD, Phobius, SosuiG v.1.1 and DAS-Tmfilter (Hirokawa et al., ; Krogh et al., ; Cserzo et al., ; Käll et al., ; Kahsay et al., ; Petersen et al., ). The PROTTER v1.0 (http://wlab.ethz.ch/protter/start/) was also used for the predic […]

library_books

Structure Prediction of Membrane Proteins

2016
PMCID: 5172438
PMID: 15629037
DOI: 10.1016/S1672-0229(04)02001-7

[…] vide a solution to the problem that non-transmembrane query sequences may give false positive hits (20%-30%) in the prediction process. The upgraded and modified version of the DAS-prediction method, DAS-TMfilter algorithm, has been distributed . The new algorithm is designed to make distinction between protein sequences with and without TM helices at a reasonably low rate of false positive predic […]

library_books

Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus

2016
mSystems
PMCID: 5111396
PMID: 27868089
DOI: 10.1128/mSystems.00065-16

[…] brane, periplasm, thylakoid membrane, thylakoid lumen, cytoplasm, or carboxysome. Protein localization was based on amino acid sequences using the PSORTb algorithm for bacteria () and the ExPASy tool DAS-TMfilter for transmembrane domain prediction (). Proteins associated with the thylakoid membranes and carboxysomes are not predicted by PSORTb and were instead inferred from homology to a detailed […]

library_books

Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes

2016
PLoS Comput Biol
PMCID: 4822843
PMID: 27049771
DOI: 10.1371/journal.pcbi.1004862

[…] [, , ], CD-HIT 4.5.7 [], Cytoscape 2.8.3 [], BLAST2SimilarityGraph plugin for Cytoscape [], Graph-0.96_01 (UnionFind) Perl library, MAFFT v7.154b [], Jalview v2.7 [], TMHMM 2.0c [], Phobius v1.01 [], DAS-TMfilter (December 2012) [], HMMER 3.0 (March 2010) [], PfamScan (October 2013) [], MEGA 5.05 [], Circos v0.64 [] and Psipred v3.5. The multiple sequence alignments were built with MAFFT-LINSI usi […]


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DAS-TMfilter institution(s)
Agricultural Biotechnology Center, Gödöllö, Hungary

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