carushi/parasor

Parallel solution for local RNA secondary structure analysis

👋 Greetings from @carushi

• 👀 Occupation: Researcher
  • Computational biology, Bioinformatics, Machine learning, and Biostatistics
• 🌱 Current projects: multi-omics analysis and image analysis
• 🌐 Lab website: https://carushi.github.io/cb_lab/

Projects

• RNA secondary structure prediction

  • ParasoR
  • reactIDR

• Omics analysis

  • Catactor
  • Meta_scATAC_shiny_server
  • yeast_coexp_analysis

• Image analysis

  • PABLO

• GUI database search

  • GoMADScan

parasor's Issues

Acessibility scores

Why are the accessibility scores sometimes greater than one? Isn't this strictly a probability normalized by the partition function, as defined in http://bioinformatics.oxfordjournals.org/content/27/13/1788.full.pdf+html?

Autoconf didn't work

$ make install
...
WARNING: 'aclocal-1.15' is missing on your system.
...

This didn't help

$ make -f _Makefile

I used a workaround as follows

$ autoreconf -ivf

Why does ParasoR Read Parameter Files (e.g., one of Turner Model) at Repository?

Hi, the developer.

I'm using the software for getting base pairing probabilities of ncRNAs.
One installed at my own user directory (e.g., under the directory $HOME/prgrms) uses the above files on the downloaded repository (e.g., under the directory $HOME/dwnlds/parasor).
I think they should be installed into the same directory as the software. (For example, if I cleaned the repository, it wouldn't run properly saying there are missing files.)
Or there are configurable settings for achieving it although I read the output from the command $ ./configure --help under the repository?

And another question: the software could use multithreading? (For example, when using the parameter "--pre", it is computing in parallel?)
If not, since I think ParasoR is one of solutions of RNA secondary structure scalable to genome data, I'd like you to implement it.