software for the exploration of lightweight stochastic context free grammars

Description:

Software developed for exploring the consequences of different single sequence SCFG designs in predicting RNA secondary structure.

Source Code:

conus-1.0.tar.gz

This is the full CONUS package (without datasets) as a gzip'ed tar ball (382 KB).

This package contains source, guides, and GNU configure script. CONUS was written in ANSI C and tested on Mandrake Linux.

[See below for a download which includes the datasets.]

Documentation:

• README
• INSTALL
• GPL LICENSE

Reference:

Dowell, RD and Eddy, SR. Evaluation of Several Lightweight Stochastic Context Free Grammars for RNA Secondary Structure Prediction. BMC Bioinformatics 5:71 (2004). [Reprint] [Abstract] [reprint (PDF)]

• Full Package (conus-1.0_all.tar.gz)
  gzip'ed tar ball (1064 KB), containing:
  • the CONUS 1.0 source code (previously described),
  • the datasets utilized in the paper (described below).
  This code corresponds exactly to the code described in the paper.
• Data Sets (notes.txt)
  • Training Set (mixed80.stk)
  • Rfam v5 Test Set (rfam5.stk)
  • Benchmarking Test Set (RNase P, SRP, tmRNA) (benchmark.stk)
• Software/Paper Guide (paperguide.txt)
  Brief description of how the CONUS programs were used to generate the results reported in the paper.