T-REKS protocols

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T-REKS specifications

Information


Unique identifier OMICS_00116
Name T-REKS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Julien Jorda <>

Information


Unique identifier OMICS_00116
Name T-REKS
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Julien Jorda <>

Publication for T-REKS

T-REKS in pipeline

2016
PMCID: 5100051
PMID: 27671125
DOI: 10.1093/molbev/msw194

[…] the corresponding hmms and joined two families into one if they are significantly similar (hhsearch e-value < 10e−5)., for each repeat family, we then reformatted the repeat annotations into the t-reks format readable by prographmsa + tr and extracted all protein sequences that correspond to it from the original alignment. we provided those sequences and the repeat annotations […]


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T-REKS in publications

 (20)
PMCID: 5293756
PMID: 28223991
DOI: 10.3389/fpls.2017.00124

[…] list of 872 proteins for r. irregularis and 2633 for g. rosea (tables , , respectively). in these repertoires, we searched for conserved domains by pfam analysis (finn et al., ), repeated motifs by t-reks analysis (jorda and kajava, ), nuclear localization by nlstradamus analysis (nguyen ba et al., ) and we scored disulfide-bond forming proteins among small cysteine-rich proteins (scr) […]

PMCID: 5274682
PMID: 28182099
DOI: 10.1155/2017/7949287

[…] significant pairwise similarity, these approaches are unable to find the latent periodicity. first of all, it involves algorithms and programs, such as trf [], mreps [], trstalker [], atrhunter [], t-reks [], imex [, ], crisprs [], swan [], and some others [, ], because similarity between the different periods is very low in case of latent periodicity. this leads to the lack of seeds […]

PMCID: 5069803
PMID: 27756311
DOI: 10.1186/s12936-016-1563-4

[…] multiple alignment with the muscle algorithm []. such alignment was manually edited to ensure correct repeat region alignment and then used for inferring dna alignment by pal2nal software []. the t-reks algorithm was used for identifying repeat regions []., dnasp v.5 software [] was used for calculating genetic diversity regarding colombian sequences and p. vivax reference sequences alignment […]

PMCID: 5100051
PMID: 27671125
DOI: 10.1093/molbev/msw194

[…] the corresponding hmms and joined two families into one if they are significantly similar (hhsearch e-value < 10e−5)., for each repeat family, we then reformatted the repeat annotations into the t-reks format readable by prographmsa + tr and extracted all protein sequences that correspond to it from the original alignment. we provided those sequences and the repeat annotations […]

PMCID: 4835772
PMID: 27091329
DOI: 10.1038/srep24638

[…] in such proteins, high cysteine residue content and tandem repeats were examined. the number of cysteine residues was identified using perl script. protein internal repeats were predicted using t-reks (http://bioinfo.montp.cnrs.fr/?r=t-reks/). the in planta localization of mature effector proteins were predicted by wolf psort (http://www.genscript.com/psort/wolf_psort.html). wolf psort […]


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T-REKS institution(s)
Centre de Recherches de Biochimie Macromoléculaire UMR, CNRS, University of Montpellier, Montpellier, France

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