LTRdigest statistics

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LTRdigest specifications

Information


Unique identifier OMICS_09457
Name LTRdigest
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data LTRdigest accepts sequence data in a variety of formats and a basic LTR annotation in GFF3 format as input. Protein domains are specified as profile HMMs in HMMER3 format.
Output data It creates GFF3 and CSV annotations as well as FASTA sequence files for all detected features.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Sascha Steinbiss <>

Publication for LTRdigest

LTRdigest in publications

 (24)
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] on the gmod site: (i) repeatmodeler with repeatscout v1.0.5, recon v1.08, repeatmasker version open4.0.5, using repbase version 20140131 () and tandemrepeatfinder; (ii) genometools ltrharvest and ltrdigest (); (iii) mitehunter with default parameters (). we generated species-specific repeat libraries for p. andersonii and t. orientalis separately and combined these into a single repeat […]

PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] the genomes of g. elata, d. officinale and p. equestris with ltrharvest from genome tools v1.5.1. the candidate sequences were filtered by two-step procedure to reduce false positives. first, ltrdigest was used to identify the primer binding site (pbs) motif based on the predicted trna sequences from trnascan-se, and only elements contained pbs were retained; then protein domains (pol, […]

PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] identified using repeatscout version 1.0.5 []. ltr regions were identified using genometools, suffixerator, ltrharvest (genometools) v1.5.1 (minimum distance 200 bp and maximum distance 5000) and ltrdigest (genometools) v1.5.1 []., de novo repeat families were searched for rip-like snp mutations [] via ripcal v2.0 [, ]. repeat family mutation sites were plotted for the highest mutation rates […]

PMCID: 5915480
PMID: 29720997
DOI: 10.3389/fgene.2018.00130

[…] nextflow pipeline (). the pipeline is available at http://doi.org/10.5281/zenodo.1098651., long terminal repeat (ltr) elements were detected using two parallel runs of the ltr harvest () and ltrdigest () packages from genometools v1.5.8 (). recent insertions of ltr elements were detected by setting the similarity cutoff in ltr harvest to 99% and only including repeats with a tgca […]

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

[…] 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 classified tes were soft-masked by repeatmasker v.4.0.6 (http://www.repeatmasker.org/) (additional file : method)., ssrs were scanned by sciroko v.3.4 [] with perfect […]


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LTRdigest institution(s)
Center for Bioinformatics, University of Hamburg, Hamburg, Germany

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