A DNA Sequence Compression Algorithm Based on LUT and LZ77

A Fixed-Length Coding Algorithm for DNA Sequence Compression

While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression programs.

多头有限状态压缩

Multihead Finite-State Compression

本文提出多头有限状态压缩模型，并证明 h 头信息无损压缩器的最优压缩比下确界等于序列的 h 头有限状态预维数，从而刻画其多头有限状态维数。

Reference Sequence Construction for Relative Compression of Genomes

Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform and also supports rapid random access to the underlying data. The main difficulty of relative compression is in selecting an appropriate reference sequence. In this paper, we explore using the dictionary of repeats generated by Comrad, Re-pair and Dna-x algorithms as reference sequences for relative compression. We show this technique allows better compression…

A constrained Shannon-Fano entropy coder for image storage in synthetic DNA

The exponentially increasing demand for data storage has been facing more and more challenges during the past years. The energy costs that it represents are also increasing, and the availability of the storage hardware is not able to follow the storage demand's trend. The short lifespan of conventional storage media -- 10 to 20 years - forces the duplication of the hardware and worsens the situation. The majority of this storage demand concerns "cold" data, data very rarely accessed but that has to be kept for long periods of time. The coding abilities of synthetic DNA, and its long durability…

Efficient Compression of Long Arbitrary Sequences with No Reference at the Encoder

In a distributed information application an encoder compresses an arbitrary vector while a similar reference vector is available to the decoder as side information. For the Hamming-distance similarity measure, and when guaranteed perfect reconstruction is required, we present two contributions to the solution of this problem. One result shows that when a set of potential reference vectors is available to the encoder, lower compression rates can be achieved when the set satisfies a certain clustering property. Another result reduces the best known decoding complexity from exponential in the vec…

Engineering Relative Compression of Genomes

Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an LZ77-style compression scheme for relative compression of multiple genomes of the same species. While the solution bears similarity to known algorithms, it offers significantly higher compression ratios at compression speed over a order of magnitude greater. One of the new successful ideas is augmenting the reference sequence with phrases from the other sequenc…