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T-RECs specifications

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Unique identifier OMICS_14710
Name T-RECs
Alternative name Tool for RECombinations
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data The query sequence(s), the annotated sequences, an annotation file of viral clusters/groups in tab-delimited format, a functional annotation file that designates potential regions of interest in the analyzed genomes.
Input format FASTA
Output data The potential recombination events visualized in a graphical window, a similarity plot, the identified genotypes, the recombination events.
Operating system Windows
Programming languages Visual Basic
Computer skills Medium
Version 0.1
Stability Beta
Requirements
USEARCH/UCLUST
Maintained Yes

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Maintainer


  • person_outline Constantinos Stathopoulos

Publication for Tool for RECombinations

T-RECs citations

 (3)
library_books

Heterogeneity of the Epstein Barr Virus (EBV) Major Internal Repeat Reveals Evolutionary Mechanisms of EBV and a Functional Defect in the Prototype EBV Strain B95 8

2017
J Virol
PMCID: 5686732
PMID: 28904201
DOI: 10.1128/JVI.00920-17

[…] these strains also show evidence of clustering of the minor variants, with different groups of mvs exhibiting different mv frequencies (table st5)., in order to analyze these variations, we used the t-recs tool to visualize the virus strains that most closely resembled both the consensus and minor variant versions of the two strains (). both trl1 and slcl-is2.01 showed evidence […]

library_books

Expression of Subtelomeric lncRNAs Links Telomeres Dynamics to RNA Decay in S. cerevisiae

2015
Noncoding RNA
PMCID: 5932542
DOI: 10.3390/ncrna1020094

[…] experiments addressing this question for terra suggested that yeast terra (yterra) transcribed from a critically short telomere functions as a scaffold for the formation of telomerase clusters (t-recs; telomerase recruitment clusters), which are subsequently recruited to telomeres []. live-cell imaging analyses of tlc1 rna revealed that telomerase nucleates emerge in g1/s phase […]

library_books

MicroRNA expression profiling predicts clinical outcome of carboplatin/paclitaxel based therapy in metastatic melanoma treated on the ECOG ACRIN trial E2603

2015
Clin Epigenetics
PMCID: 4457092
PMID: 26052356
DOI: 10.1186/s13148-015-0092-2

[…] microarrays (ht12 v4) (mrna expression) with protocols optimized for ffpe samples. integrative computational analysis was performed using a novel tree-guided recursive cluster selection (t-recs) [1] algorithm to select the most informative features/genes, followed by targetscan mirna target prediction (human v6.2) and mirconnx [2] for network inference., t-recs identified plxnb1 […]


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T-RECs institution(s)
Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece; Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece; Faculty of Life Sciences, University of Manchester, Manchester, UK
T-RECs funding source(s)
This work has been supported under the "ARISTEIA II" Action of the "OPERATIONAL PROGRAMME EDUCATION AND LIFELONG LEARNING" and is co-funded by the European Social Fund (ESF) and National Resources and also supported by the research grants from the Postgraduate Programme ‘Applications of Molecular Biology-Genetics, Diagnostic Biomarkers’ of the University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology.

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