Hi all, do you know where I can find tRNA gene annotations in Oryza sativa? I need the annotations tRNA anticodons. However, there is no such annotations in Ensembl gff3 or gtf file. I can find detailed annotations in Genomic tRNA database: http://gtrnadb.ucsc.edu/Osati/, but the genome version is not what I want.
Hope there will be better solutions, thanks very much.
You may be able to transfer the annotations, but I would personally just run the analysis locally since rice has a small genome (for plants). The database was generated with the program tRNAscan-SE, and it is pretty easy to use. The easiest way to do this though is with MAKER, which can be configured with the path to the program and you will get a gff3 as a result. There is no need to run other annotation programs, so I would try to pass through just tRNAscan-SE and have MAKER do the work for you.
I should have clarified that comment, sorry about that. MAKER is a separate software package for annotating genomes. To run it locally you will first use the command maker -CTL to generate the configuration files. Then, edit the "maker_exe.ctl" file and specify the path to tRNAscan-SE. The genome file is specified in the "maker_opts.ctl" file. The output will be a gff3 file with the coordinates of the tRNAs.
Thank you very much. I'm running tRNAscan-SE now. Can you introduce more about MAKER? I didn't see MAKER in the help.
I should have clarified that comment, sorry about that. MAKER is a separate software package for annotating genomes. To run it locally you will first use the command
maker -CTLto generate the configuration files. Then, edit the "maker_exe.ctl" file and specify the path to tRNAscan-SE. The genome file is specified in the "maker_opts.ctl" file. The output will be a gff3 file with the coordinates of the tRNAs.Oh, thank you. I will have a try of MAKER.