BiobaseXNA: biological sequences

This is a base library for dealing with (short) biological sequences. Longer sequences should be imported via different Biobase libraries and streamed in short windows.

README

(included from project) Christian Höner zu Siederdissen - BiobaseXNA

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BiobaseXNA

Efficient encoding of (short) biological sequences. This package ist designed to deal with in-memory snippets of DNA, RNA, and amino acids. The encoding is geared toward time-efficiency, not necessarily space efficiency (we use Int’s for encoding characters, not the smallest type possible).

Additional modules provide conversion capabilities between different types of characters according to biological laws, and some biochemical constraint information. The latter includes canonical and non-canonical pairing information for RNA.

Actual energy parameters for pairings are provided by other packages, for example BiobaseTurner for the loop energy model with measured parameters.

Contact

Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
http://www.bioinf.uni-leipzig.de/~choener/

hackage
 sources
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Stable Sources git Bugtracker Build Status

Usage of this library in a Haskell project:

This package provides no "main" executable, but rather only library functionality. (Though sometimes tools, or example programs are provided). Usage requires some knowledge of Haskell.
  1. Include the library in your cabal file.
  2. Use stack to simplify development. This will require adding the library with an exact version to the stack.yaml file. This includes the option to include this library directly from its github repository.