TEclass protocols

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TEclass specifications

Information


Unique identifier OMICS_15033
Name TEclass
Interface Web user interface
Restrictions to use None
Input data Genomic sequences
Input format FASTA
Output data The classification of the transposable element.
Programming languages Perl
Computer skills Basic
Stability Stable
Source code URL http://www.compgen.uni-muenster.de/tools/teclass/download/TEclass-2.1.3.tar.gz
Maintained Yes

Maintainer


  • person_outline György Abrusán <>

Information


Unique identifier OMICS_15033
Name TEclass
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Genomic sequences
Input format FASTA
Output data The classification of the transposable element.
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Version 2.1
Stability Stable
Requirements
BASH, Python, gcc, GNU make
Source code URL http://www.compgen.uni-muenster.de/tools/teclass/download/TEclass-2.1.3.tar.gz
Maintained Yes

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Maintainer


  • person_outline György Abrusán <>

Publication for TEclass

TEclass in pipeline

2017
PMCID: 5651803
PMID: 29057900
DOI: 10.1038/s41598-017-13807-0

[…] server. analysis of k-mer frequency distributions were done in jellyfish and the assembly of repeatable dna was done in tedna , the provisional classification of the assembled elements was done by teclass. all mapping and manipulation of genomic reads were done in clc genomics workbench., agata weydmann and artur burzyński contributed equally to this work., publisher's note: springer nature […]


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TEclass in publications

 (21)
PMCID: 5651803
PMID: 29057900
DOI: 10.1038/s41598-017-13807-0

[…] server. analysis of k-mer frequency distributions were done in jellyfish and the assembly of repeatable dna was done in tedna , the provisional classification of the assembled elements was done by teclass. all mapping and manipulation of genomic reads were done in clc genomics workbench., agata weydmann and artur burzyński contributed equally to this work., publisher's note: springer nature […]

PMCID: 5412055
PMID: 28464870
DOI: 10.1186/s12864-017-3699-1

[…] or reduction in scaffold number., the assembled genomes were masked before gene prediction using a customized pipeline which included repeatmasker-open-3-3-0, repbase [], repeatscout [], trf [] and teclass []. fungal genes downloaded from ncbi (august, 2012) were mapped to the vi1 genome assembly using exonerate [] for similarity based gene prediction. transcriptome assemblies for in planta […]

PMCID: 5437944
PMID: 28369349
DOI: 10.1093/gigascience/giw004

[…] analysis, repeatmodeler [] was used to construct a te library. elements within the library were then classified using a homology search with repbase and a support vector machine (svm) method (teclass) []. a total of 44.3 % of the s. furcifera genome consists of tandem repeats and tes (table ); lower than the brown planthopper (48.6 %) but much higher than the pea aphid (33.3 %). class […]

PMCID: 5118889
PMID: 27875982
DOI: 10.1186/s12864-016-3299-5

[…] library of interspersed repeat families as input for repeatmasker []. repeatmasker was also used to find and mask genomic regions of low complexity. we applied the automated classification tool teclass [] to categorize the predicted repeat sequences into the four main transposable element categories dna transposon, long interspersed nuclear element (line), short interspersed nuclear element […]

PMCID: 5117676
PMID: 27871234
DOI: 10.1186/s12864-016-3302-1

[…] blastx with an e-value cutoff of 1e-06, and then the repeats containing hits to transposon related proteins were eliminated from the list of novel repeats. the novel repeats were classified using teclass [], and then were used as a custom library for repeatmasker to further mask repetitive sequences in the sweetpotato bess., the sweetpotato bess without known and novel repeats were analyzed […]


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TEclass institution(s)
Katholieke Universiteit Leuven, Department of Biology, Laboratory of Aquatic Ecology and Evolutionary Biology, Leuven, Belgium; University of Münster, Faculty of Medicine, Institute of Bioinformatics, Münster, Germany
TEclass funding source(s)
Katholieke Univeristeit Leuven Belgium (post-doctoral fellowship), University of Münster Germany

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