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Protocols

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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Versioning


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Maintainer


  • person_outline György Abrusán

Publication for TEclass

TEclass citations

 (16)
call_split

Mitochondrial genomes of the key zooplankton copepods Arctic Calanus glacialis and North Atlantic Calanus finmarchicus with the longest crustacean non coding regions

2017
Sci Rep
PMCID: 5651803
PMID: 29057900
DOI: 10.1038/s41598-017-13807-0
call_split See protocol

[…] b 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. […]

library_books

Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

2017
BMC Genomics
PMCID: 5412055
PMID: 28464870
DOI: 10.1186/s12864-017-3699-1

[…] 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 and […]

library_books

The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases

2017
BMC Genomics
PMCID: 5327563
PMID: 28241794
DOI: 10.1186/s12864-017-3574-0

[…] pping matches in RepeatModeler and homology searches. For comparative genomic analyses, we selected sequences with more than 50% of coverage of consensus repetitive sequences and classified them with TEclass software (a tool for automated classification of unknown eukaryotic transposable elements []). Sequences from RepeatModeler and from reported Echinococcus species entries were remapped on the […]

library_books

Comparative “Omics” of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis

2016
Genome Biol Evol
PMCID: 5203792
PMID: 28040774
DOI: 10.1093/gbe/evw259

[…] lements using RepeatScout () followed by an assessment of known repeat elements. According to RepBase () transposable elements were classified into the four main transposable element categories using TEclass: DNA transposon, long interspersed nuclear element (LINE), short interspersed nuclear element (SINE), and retrotransposon with long terminal repeats (LTRs) (). The FFC members examined had an […]

library_books

Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment

2016
Mol Biol Evol
PMCID: 5854124
PMID: 28007977
DOI: 10.1093/molbev/msw230

[…] aining two de novo repeat-finding programs, RECON () and RepeatScout (). The repetitive elements were then classified using homologous searches with Repbase and a Support Vector Machine (SVM) method (TEClass). There is no linkage map available for L. waleckii so far. As the O. latipes genome maintains the teleost ancestral genome karyotypes, we selected the O. latipes genome () as a reference to c […]

library_books

Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species

2016
Sci Rep
PMCID: 4858695
PMID: 27151494
DOI: 10.1038/srep25591

[…] meters, which generated consensus sequences and classification information for each repeat family. Two different results were merged and redundant sequences were removed by blastn and classified with TEclass. RepeatMasker (version 3.3.0) (http://www.repeatmasker.org/) has been used to search for TE in genome with our library. The copy number variation of transposon elements was analyzed based on R […]

Citations

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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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