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REPCLASS specifications

Information


Unique identifier OMICS_19030
Name REPCLASS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A DNA sequence.
Input format FASTA
Output data An indicative of retroposed element.
Output format TXT
Operating system Unix/Linux
Programming languages Perl
License Academic Free License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for REPCLASS

REPCLASS citations

 (12)
library_books

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

2018
BMC Genomics
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] TEs in reference assembly were predicted using RepeatScout v.1.0.5 [], Nseg [], TRF [] and classified with REPCLASS v.1.0.1 [] and tblastx against Repbase Update database v.29.8.2016. Full-length long terminal repeat (LTR) retrotransposons were identified by LTRharvest [] and LTRdigest []. All detected cla […]

library_books

Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia)

2018
PMCID: 5940132
PMID: 29519939
DOI: 10.1534/g3.117.300443

[…] rminal inverted repeats (TIRs), and detection of target site duplications (TSDs). Homology-based evidence was obtained using RepeatMasker (), as well as the homology module of the TE classifying tool RepClass (). RepClass was also used to identify signatures of transposable elements (TIRs, TSDs). We then eliminated non-TE repeats (simple repeats or gene families) using custom Perl scripts (availab […]

library_books

Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories

2017
Mob DNA
PMCID: 5718144
PMID: 29225705
DOI: 10.1186/s13100-017-0103-2

[…] rce for homology-based RepeatMasker annotation, which has a built-in classification tool, and employs four major subclasses (DNA, LTR, ERV, non-LTR), with further subdivisions into superfamilies. The RepClass classification tool employs four subclasses (DNA, LTR, non-LTR, Helitron), and identifies class (C), subclass (SC), and superfamily (SF), accounting for homology, structural features, and TSD […]

library_books

Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction

2017
BMC Genomics
PMCID: 5483258
PMID: 28646875
DOI: 10.1186/s12864-017-3860-x

[…] ion 3.1-snap20121016.1 and TRF version 4.0.4) and 17.4% of the 511 scaffolds (after cleaned up) were masked by the de novo modeled repeats or simple repeats. The 754 repeat sequences were analyzed by REPCLASS [] (version 1.0.1 with RepBase version 22.03, blast version 2.3.0, options for tblastx: -evalue 0.0001 -num_descriptions 10,000,000 -num_alignments 10,000,000 -seg yes and options for blastn: […]

library_books

Stella modulates transcriptional and endogenous retrovirus programs during maternal to zygotic transition

2017
eLife
PMCID: 5404928
PMID: 28323615
DOI: 10.7554/eLife.22345.035

[…] ptional NH tags of all alignments in the SAM files were set to one and mapped reads were counted for each TE using htseq-count (). We show multi-mapped reads can be unambiguously assigned to a class (repClass in RepeatMasker) and family (repFamily in RepeatMasker) 98% of the time, however, only 54% of the time at the level of an element (repName in RepeatMasker) (). For this reason, all analysis a […]

library_books

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

2016
eLife
PMCID: 5182062
PMID: 27892853
DOI: 10.7554/eLife.19090.045

[…] and detection of Target Site Duplications (TSDs). Homology-based evidence was obtained using RepeatMasker Protein Mask () (RRID:SCR_012954), as well as the homology module of the TE classifying tool RepClass () (RRID:SCR_014654). Repclass was also used to identify some of the signatures of transposable elements (TIRs, TSDs). We then eliminated non-TE repeats (simple repeats or gene families). Fir […]

Citations

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REPCLASS institution(s)
Department of Biology, University of Texas, Arlington, TX, USA ; Department of Computer Sciences and Engineering, University of Texas, Arlington, TX, USA
REPCLASS funding source(s)
Supported by National Institutes of Health (R01GM77582) and National Science Foundation (EIA-0216500).

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