The Biobase Library

Overview

Biobase contains functions for dealing with special file formats relevant for the task of RNA secondary structure determination.

Functionality

Transform strings/bytestrings into an internal ‘string’ format. Read in and write out Turner and Vienna RNA / DNA parameter files. Read Infernal covariance model (CM) files. Parts of the library dealing with RNA are optimized for speed, using newtypes and Data.Vector.Unboxd internally; parts dealing with CMs are not optimal when it comes to speed.

Future

  • in the long run, I want to use the Fasta reader from bio
  • some functions are still rather ad-hoc and need more functionality
  • in spring 2011: more functions for handling RNA, Stockholm files, covariance models
  • “DataSource”s will come soon, allowing users to easily and efficiently load some common formats (except fasta which is provided by “bio”)