TIGR Plant Repeat Databases statistics

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TIGR Plant Repeat Databases specifications

Information


Unique identifier OMICS_03248
Name TIGR Plant Repeat Databases
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/TIGR_plant_repeat_database

Publication for TIGR Plant Repeat Databases

TIGR Plant Repeat Databases citations

 (4)
library_books

Dynamic Evolution of Rht 1 Homologous Regions in Grass Genomes

2013
PLoS One
PMCID: 3782514
PMID: 24086561
DOI: 10.1371/journal.pone.0075544

[…] on of BAC sequences, all known repetitive elements were first identified through BLAST searches against the database for Triticeae repetitive elements (TREP) (http://wheat.pw.usda.gov/ITMI/Repeats/), TIGR Plant Repeat Databases (http://plantrepeats.plantbiology.msu.edu/index.html) and RepeatMasker (http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker). Their annotation was next performed with minor […]

call_split

Transcriptional activity of transposable elements in maize

2010
BMC Genomics
PMCID: 3091746
PMID: 20973992
DOI: 10.1186/1471-2164-11-601
call_split See protocol

[…] Model TE sequences were obtained from the TIGR Plant Repeat Databases [], Retrotransposon Database [] and GeneBank. Only well characterized elements were included in our analysis (Table ). Model sequences were compared with the maize (Zea may […]

library_books

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

2008
BMC Plant Biol
PMCID: 2565679
PMID: 18803819
DOI: 10.1186/1471-2229-8-95

[…] , RepeatMasker [] with the CrossMatch algorithm and default settings was used to search repeats without specifying a custom library. Thereafter, sequences were searched against TREPtotal, RepBase and TIGR Plant Repeat Databases. In the second step sequences were searched using TBLASTX (E-value = 1e-5) [] against the same databases. Sequences matching known repeats were masked with an "X". Putative […]

library_books

LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice

2008
BMC Genomics
PMCID: 2533021
PMID: 18691433
DOI: 10.1186/1471-2164-9-382

[…] quencing Resources website (Version 1.0. Released on July, 2006) [].A database of known legume LTR retrotransposons was constructed by extracting legume elements from literatures [,-], Repbase [] and TIGR Plant Repeat Databases []. This database was used to discriminate previously reported families from novel ones discovered in this research. A Mt tRNA database was also built by scanning the genom […]

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TIGR Plant Repeat Databases institution(s)
The Institute for Genomic Research, Chinakville, MD, USA

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