mxfold2
mxfold2 copied to clipboard
mxfold
MXfold2: RNA secondary structure prediction using deep learning with thermodynamic integration
Hi, I am wondering if you could clarify what the output from mxfold2 represents? Specifically the numbers in the parenthesis at the bottom right? Are these a score or metric...
Hi, can you provide instructions for building from source the latest in this repo? Thank you!
Hello Developers, I’m trying to use `mxfold2` to predict for some RNA sequences. However, I encountered a inconsistent result between my local prediction and the web service at `http://www.dna.bio.keio.ac.jp/mxfold2/predict` as...
About mxfold2-0.1.1.tar.gz and mxfold2-0.1.2.tar.gz. The former install successfully but not the latter on Windows. What could be the reason? An unsuccessful installation of the latter comes with the following message:...
I cloned the repository into my university's cluster. To work around importing issues and get things working properly, I put this file in my home directory: ```python # Called `mf2`...
I can't find how to change the batch size. With the param in the default, the training is so slow, so how can I change the batch size to speed...
Hi, I was wondering if there is any way to predict structures of sequences > 1000 nt? I have only used the web server, if using the command line tools...
Hi, I retrain the model with the default hyper-param, but the recall is 0.63, with the default param, the recall is 0.685, which will cause this different? Thanks.
I can't get mxfold2 to run on my MacBook at all. Here's what happens: ``` BenjaminLee@mbp ~/r/viroid-search (master) [SIGSEGV]> clang --version (viroid-search) Apple clang version 14.0.0 (clang-1400.0.29.202) Target: x86_64-apple-darwin22.1.0 Thread...
Changing `--model` or `--seed` doesn't change the output for either the .bpp or .bpseq file. Is this expected?
