Issue No. 03 - July-September (2007 vol. 4)
This article introduces an algorithm for the lossless compression of DNA files, which contain annotation text besides the nucleotide sequence. First a grammar is specifically designed to capture the regularities of the annotation text. A revertible transformation uses the grammar rules in order to equivalently represent the original file as a collection of parsed segments and a sequence of decisions made by the grammar parser. This decomposition enables the efficient use of state-of-the-art encoders for processing the parsed segments. The output size of the decision-making process of the grammar is optimized by extending the states to account for high-order Markovian dependencies. The practical implementation of the algorithm achieves a significant improvement when compared to the general-purpose methods currently used for DNA files.
4 [Data]: Coding and Information Theory | Data compaction and compression, F.4 [Theory of Computation]: Mathematical Logic and Formal Languages | Formal languages, G.3 [Mathematics of Computing]: Probability and Statistics | Markov processes, J.3 [Computer Applications]: Life and Medical Sciences | Biology and genetics, Annotation, Compression, Formal Grammars, Nucleotide sequences
Gergely Korodi, Ioan Tabus, "Compression of Annotated Nucleotide Sequences", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, no. , pp. 447-457, July-September 2007, doi:10.1109/tcbb.2007.1017