PRED-TAT protocols

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PRED-TAT specifications

Information


Unique identifier OMICS_03890
Name PRED-TAT
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pantelis G. Bagos <>

Publication for PRED-TAT

PRED-TAT in pipelines

 (4)
2017
PMCID: 5276818
PMID: 28194142
DOI: 10.3389/fmicb.2017.00087

[…] the ncbi sequence databases. the transmembrane helices were predicted with tmhmm server v. 2.0. the n-terminal signal peptides were predicted using signal p v.4.1 for gram-negative bacteria and pred-tat., amino acid sequences were transferred into the mega 6.0 software suite, and aligned using clustal w. amino acid sequences of napa were downloaded from genbank. the aligned amino acid […]

2016
PMCID: 4911364
PMID: 27379079
DOI: 10.3389/fmicb.2016.00950

[…] were found by rnammer server (). signal peptides were predicted using signal p v.4.1 for gram-negative bacteria. the n-terminal twin-arginine translocation (tat) signal peptides were predicted using pred-tat, the transmembrane helices – with tmhmm server v. 2.0., for phylogenetic analysis of the catalytic a subunits of molybdopterin oxidoreductases the t. dismutans proteins tdis_0362, tdis_0614, […]

2016
PMCID: 5080606
PMID: 27782174
DOI: 10.1038/srep35990

[…] dependent]) or clade ii (noszi [nitrous_nosz_gp; sec dependent]) based on conserved protein domains using cd-search. classification was confirmed by detection of signal peptides using the pred-tat algorithm. taxonomy for each reference sequence was retrieved from ncbi using accession numbers associated to reference sequences. metagenome extracted nosz sequences were annotated […]

2012
PMCID: 3551663
PMID: 23259483
DOI: 10.1186/1471-2164-13-723

[…] and validation of metabolic pathways was curated manually., the multiple sequence alignment was perfomed with the clustalw [] and default settings were used. tat motif prediction was performed with pred-tat []., motility was tested with two different methods. first, the motility of free-swimming cells was assayed under oxic conditions immediately after taking samples. second, in order to force […]


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PRED-TAT in publications

 (39)
PMCID: 5928048
PMID: 29712968
DOI: 10.1038/s41598-018-25146-9

[…] were predicted using signal p v.4.1 for gram-positive bacteria (http://www.cbs.dtu.dk/services/signalp/). the n-terminal twin-arginine translocation (tat) signal peptides were predicted using pred-tat (http://www.compgen.org/tools/pred-tat/) and the transmembrane helices with tmhmm server v. 2.0 (http://www.cbs.dtu.dk/services/tmhmm/)., the values of dna-dna hybridization in silico […]

PMCID: 5875014
PMID: 29598818
DOI: 10.1186/s12934-018-0901-3

[…] probability that they in fact really do so []., for the identification of tat signal peptides, tatp (http://www.cbs.dtu.dk/services/tatp/ []), tatfind (http://signalfind.org/tatfind.html []), and pred-tat (http://www.compgen.org/tools/pred-tat/ []) are commonly used prediction programs. however, since twin-arginine residues can also occur in sec signal peptides, these programs tend somewhat […]

PMCID: 5924526
PMID: 29597294
DOI: 10.3390/genes9040184

[…] tat and sec genes in the genome of h. elongata dsm 2581t []. the copper resistance protein pcoa (helo_1864) made a promising candidate with congruent identification of a tat leader peptide by pred-tat [] and tatp1.0 []: msmpqkpllpltrrqllkggsalgistmalglppawa-spwg (twin-arginin motif and cleavage site underlined). already well investigated is the periplasmatic ectoine binding protein teaa […]

PMCID: 5799272
PMID: 29449848
DOI: 10.3389/fpls.2017.02242

[…] of molecular genetics and cell biology, university of chicago, chicago, il, united states. signal peptides of the e. coli k-12 tort (aac74079.1) and tora (np_415517.1) proteins were identified using pred-tat (), and dna coding sequences for the peptides were used without modification., the dna sequence of the amaranthus hybridus ppsba promoter () was kindly provided by dr. kirankumar mysore, […]

PMCID: 5768637
PMID: 29375498
DOI: 10.3389/fmicb.2017.02592

[…] et al., ) with gram-negative bacteria models. in addition, the presence of n-terminal signal peptides, the position of their cleavage site, and the corresponding export pathway were investigated by pred-tat (bagos et al., ). theoretical isoelectric point and molecular weight of the predicted precursor and mature protein forms were computed from their respective sequence by protparam tool […]


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PRED-TAT institution(s)
Department of Computer Science and Biomedical Informatics, University of Central Greece, Lamia, Greece

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