The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants

By Ouyang Shu, C. R. Buell. Nucleic Acids Res., 2004

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Progress towards a reference genome for sunflower (2011, methodology): “…were identified using RepeatScout (Price et al. 2005), annotated using The Institute for Genomic Research (TIGR) all plant repeat database (Ouyang and Buell 2004), and used as a custom library for RepeatMasker (http://repeatmasker.org; A.F.A. Smit and P. Green, RepeatMasker, version…”
The TIGR Rice Genome Annotation Resource: improvements and new features (2006, methodology): “At the functional annotation level, we provided more thorough identification of transposable element (TE)-related gene models by updating the TIGR Oryza Repeat Database (18).”
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments (2007, methodology): “Repeats were masked using RepeatMasker [50] and the rice repeat library [51].”
Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics (2013, methodology): “…genes from the annotation data set, we masked repetitive sequences in the transcript sequences using CENSOR (Kohany et al. 2006) with the MIPS Repeat Element Database (Spannagl et al. 2007) and the Plant Repeat Databases version 3 of Michigan State University (Ouyang and Buell 2004).”
The genome of woodland strawberry (Fragaria vesca) (2010, unknown): “and the Institute for Genomic Research (TIGR) repeat databas”