Benchmarking results of HiTE

TE annotation libraries used in the benchmarking of HiTE

The TE libraries generated by HiTE, EarlGrey, RepeatModeler2, EDTA, and RepeatScout are located in the directories:

• benchmark/HiTE_lib
• benchmark/EarlGrey_lib
• benchmark/rm2_lib
• benchmark/EDTA_lib
• benchmark/RS_lib

Novel TIR elements of Rice

1. HiTE discovers over 1000 novel TIR elements of rice with well-defined structures that are not included in known libraries, stored in the directory novel_tir_rice.
2. You can find the multiple sequence alignment files for each of the novel TIR elements in novel_tir_rice/msa.zip file, and the structural definitions for each transposon in the data.xlsx file.
3. With these information, you can easily determine the structural features of novel TIR elements and validate their reliability. The following figure shows a novel TIR transposons identified by HiTE, visualized using MEGA.

Novel TIR and Helitron elements in the centromeres of Maize

1. We conducted a comparative analysis between HiTE and the Maize TE Consortium (MTEC) library on TIR and Helitron transposons in centromeres of a complete telomere-to-telomere assembly of the maize genome (doi:10.1038/s41588-023-01419-6), as shown in the following figure.
2. The positions of novel TIR and Helitron elements in the centromere (data.xlsx), along with their multiple sequence alignment results (*_msa.zip), are stored in the directory novel_tir_helitron_maize_centromeres.

RepeatMasker_Lib.zip

RepeatMasker_Lib.zip is used to replace the Dfam library in RepeatMasker, refer to this page for more information.