Open lyysxb opened 1 week ago
Hi,
Thank you for using HELIANO.
I am not sure if I understand correctly to your question. To detect nonautonomous Helitron insertions, HELIANO firstly identify the significantly co-occuring LTS-RTS pairs in a given genome. After obtaining the LTS-RTS pairs, HELIANO will recover the nonauto coordination based on the coord of LTS and RTS.
All the best, Zhen
I used HELIANO to test the genomes of peanut, corn and strain Fo5176 mentioned in the example, using the parameters provided in usage heliano -g test.fa -is1 0 -is2 0-o test_opt -w 15000 I have the following questions and would like to ask you:
Best, Zhen
Thank you very much for your reply! I have discussed this with my senior and teacher, and their opinions are exactly the same as your reply. Accurately identifying Helitron transposons is one of the necessary parts of my project. Your tool is very valuable to me. In order to better play its role, if it is convenient for you, can you upload the development version of HELIANO or send it to the mailbox 65520407@qq.com? We want to train the HMM model and try to find some Helitron with less degradation. Thanks!
You said you want to find Helitron with less degradation. Do you mean young Helitrons with complete structures? If that is your question, then I don't understand why you need a HMM model to do that job. Anyway, the HMM model (RepHel.hmm) for HELIANO is avaliable within its package. You can also download it from this repository. This model is only used for scanning and classifying Helitron-like transposases.
Hi,
Thank you very much for your open source contribution. I would like to ask how the 'noauto' Helitron is detected in this code, and specifically, in which method is it implemented?