Abstract
The development of high-throughput sequencing technology has generated huge amounts DNA data. Many general compression algorithms are not ideal for compressing DNA data, such as the LZ77 algorithm. On the basis of Nour and Sharawi’s method,we propose a new, lossless and reference-free method to increase the compression performance. The original sequences are converted into eight intermediate files and six final files. Then, the LZ77 algorithm is used to compress the six final files. The results show that the compression time is decreased by 83% and the decompression time is decreased by 54% on average.The compression rate is almost the same as Nour and Sharawi’s method which is the fastest method so far. What’s more, our method has a wider range of application than Nour and Sharawi’s method. Compared to some very advanced compression tools at present, such as XM and FCM-Mx, the time for compression in our method is much smaller, on average decreasing the time by more than 90%.
Highlights
The advent of high-throughput sequencing technology has led to a dramatic increase in the size of DNA data
We selected ten genomes with different lengths (1~15 M) from the NCBI(National Center of Biotechnology Information) database as a test data set, all data comes from “http://www.ncbi. nlm.nih.gov”, the data are collected by myself. They are tested on compression ratio, compression time and decompression time
As the amount of DNA data continues to grow, we believe that he LZ77 algorithm, will play a key role in DNA data compression due to their simplicity and applicability
Summary
The advent of high-throughput sequencing technology has led to a dramatic increase in the size of DNA data. The GeNML algorithm proposed by Tabus and Korodi [6] uses a special normalized maximum likelihood discrete regression model [7] (NMLComp, characterized by low spatial complexity) as a key part of the algorithm It uses coding blocks and combines with the alternative principle to achieve compression of DNA data. In the first step of the first compression phase, the first 1000 base characters are taken from original sequence as a sample, the frequencies of four base characters A, T, G, and C are calculated and sorted them in descending order. If the first step is applied, the binary lengths obtained in the three files are 30 (nine 1 and twenty one 0), 21 (eight 1 and thirteen 0) and 13 (seven 1 and six 0), so 64 bits are needed to store 30 base characters. Use the LZ77 algorithm to decompress files (f1aa, f1bb, f2aa, f2bb, f3 and f0)
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