rice7.0.0.liban is the manually curated rice TE database. It includes LTR retrotransposons, non-LTR retrotransposons (SINEs and LINEs), DNA transposons (autonomous TIR elements, nonautonomous TIR elements, MITEs, and Helitrons), the rice centromeric repeat (Os1304#Centro/tandem) and the satellite repeat (Os2182#Satellite/rice). In addition, the LTR, SINE, LINE, TIR, and Helitron sublibraries were also provided. This library is obtained from the riceTElib.
maizeTE11122019 is the Maize TE Consortium (MTEC) curated TE library created in 2014/10/10 and updated in 2019/11/12. The original sequence names were converted to fit the naming scheme of RepeatMasker, so that TEs could be parsed into class, superfamilies, and families. A TE-free whole-genome CDS dataset derived from the B73v4 annotation was used to clean any potential genic sequences in this MTEC library. TE sequences containing more than 1000 bp or 30% of genic sequences were discarded entirely, otherwise genic sequences were removed and the remaining sequences were joined. Cleaned TE sequences shorter than 80 bp were also discarded. As terminal structure of TEs is the key for their identification, any TE sequences with the beginning or ending 20 bp masked by CDS sequences were determined false positives and removed. Two elements, teki_AC202867-7492#LTR/unknown and chr3-D-28761151#LTR/Copia, were determined incorrect based on curations and removed. In addition, the rDNA spacer (AF013103.1), the subtelomere 4-12-1 (CL569186.1), and the consensus knob180, TR-1, and CentC squences provided by Jianing Liu were added to this library. Overall, a total of 1,362 sequences were included (original 1,546).
Rice_MSU7.fasta.std7.0.0.out is the whole-genome TE annotation of the rice genome (MSUv7) based on the rice7.0.0.liban library. This command was used to generate the file:
RepeatMasker -pa 100 -div 40 -cutoff 225 -lib rice7.0.0.liban Rice_MSU7.fasta
HelitronScanner.training.set.fa is 100 bp head and tail sequences from curated Helitrons obtained from the HelitronScanner package. Sequences were first masked using the rice6.9.5.liban library to filter out non-Helitron sequences, then sequence names were renamed to fit the RepeatMasker sequence name length requirement.
Tpases020812DNA is the DNA TE transposase database obtained from the LTR_retriever package.
Tpases020812LINE is the LINE retrotransposase database obtained from the LTR_retriever package.
alluniRefprexp082813 is the unique plant protein transposase database obtained from the LTR_retriever package. For non-plant species, you may use uniport_sprot databases instead.
dummy060817.fa just a random sequence copied from the LTR_retriever package. It is used to test run RepeatMasker.