BiobaseXNA: Efficient RNA/DNA/Protein Primary/Secondary Structure

[ bioinformatics, bsd3, library, program ] [ Propose Tags ]

This is a base library for bioinformatics with emphasis on RNA and DNA primary structure as well as amino acid sequences.

Provided are efficient encodings for short (limited by the amount of RAM) sequences, as required by RNA folding tools. Extended RNA secondary structures can be represented as well.

Contains data from:

Frequency and isostericity of RNA base pairs
Jesse Stombaugh, Craig L. Zirbel, Eric Westhof, and Neocles B. Leontis
Nucl. Acids Res. (2009)

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Dependencies aeson (>=1.0), attoparsec (>=0.13), base (>=4.7 && <5.0), bimaps (>=0.1.0 && <0.1.1), binary (>=0.7), BiobaseENA (>=0.0.0 && <0.0.1), BiobaseTypes (>=0.2.1 && <0.2.2), BiobaseXNA, bytes (>=0.15), bytestring (>=0.10), cereal (>=0.4), cereal-vector (>=0.2), cmdargs (>=0.10), containers (>=0.5), csv (>=0.1), data-default (>=0.7), deepseq (>=1.3), DPutils (>=0.1.1 && <0.1.2), file-embed (>=0.0.8), ForestStructures (>=0.0.1 && <0.0.2), hashable (>=1.2), lens (>=4.0), mtl (>=2.0), primitive (>=0.5), PrimitiveArray (>=0.10.1 && <0.10.2), QuickCheck (>=2.7), split (>=0.2), text (>=1.0), tuple (>=0.3), vector (>=0.11), vector-binary-instances (>=0.2), vector-th-unbox (>=0.2) [details]
License BSD-3-Clause
Copyright Christian Hoener zu Siederdissen, 2011 - 2021
Author Christian Hoener zu Siederdissen
Category Bioinformatics
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Source repo head: git clone git://
Uploaded by ChristianHoener at 2021-06-04T20:20:23Z
Reverse Dependencies 17 direct, 2 indirect [details]
Executables SubOptDistance
Downloads 31051 total (49 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2021-06-04 [all 1 reports]

Readme for BiobaseXNA-

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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.


Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany