LTR_STRUC protocols

LTR_STRUC specifications

Information


Unique identifier OMICS_09458
Name LTR_STRUC
Alternative name LTR retrotransposon structure program
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Sequence
Input format FASTA, NCBI
Operating system Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Vinay Mittal <>

Publication for LTR retrotransposon structure program

LTR_STRUC IN pipelines

 (3)
2014
PMCID: 4029996
PMID: 24849372
DOI: 10.1371/journal.pone.0097099

[…] a “plasticity ratio”., the distribution of full-length del elements and u3 att matches were examined in the two genomes (sorghum and maize) with the highest copy number of elements, according to the ltr_struc output. to map full-length copies, data was taken from the ltr_struc output, which included the source of the ltr-rt, in this case, the chromosome from which the sequence came from. to map […]

2014
PMCID: 4029996
PMID: 24849372
DOI: 10.1371/journal.pone.0097099

[…] u3 att matches were examined in the two genomes (sorghum and maize) with the highest copy number of elements, according to the ltr_struc output. to map full-length copies, data was taken from the ltr_struc output, which included the source of the ltr-rt, in this case, the chromosome from which the sequence came from. to map u3 att sites, the conserved 5′ ltr ten base pair region (the 5′ att […]

2007
PMCID: 1950507
PMID: 17650302
DOI: 10.1186/1471-2164-8-247

[…] sequences. they were downloaded from the ncbi website [13] and represent ~1 650 mb., the ab initio identification of ltr retrotransposons within the rice and maize sequences was performed by the ltr_struc software [9] using standard specifications. all of the 4072 potential complex elements output by this program were first screened by a home-made python script according to their size, […]

LTR_STRUC institution(s)
Department of Genetics, University of Georgia, Athens, GA, USA

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