Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes

Abstract

An efficient DNA compressor furnishes an approximation to measure and compare information quantities present in, between and across DNA sequences, regardless of the characteristics of the sources. In this paper, we compare directly two information measures, the Normalized Compression Distance (NCD) and the Normalized Relative Compression (NRC). These measures answer different questions; the NCD measures how similar both strings are (in terms of information content) and the NRC (which, in general, is nonsymmetric) indicates the fraction of one of them that cannot be constructed using information from the other one. This leads to the problem of finding out which measure (or question) is more suitable for the answer we need. For computing both, we use a state of the art DNA sequence compressor that we benchmark with some top compressors in different compression modes. Then, we apply the compressor on DNA sequences with different scales and natures, first using synthetic sequences and then on real DNA sequences. The last include mitochondrial DNA (mtDNA), messenger RNA (mRNA) and genomic DNA (gDNA) of seven primates. We provide several insights into evolutionary acceleration rates at different scales, namely, the observation and confirmation across the whole genomes of a higher variation rate of the mtDNA relative to the gDNA. We also show the importance of relative compression for localizing similar information regions using mtDNA.

Visual Analysis of Research Paper Collections Using Normalized Relative Compression

“…More concretely, they use relative entropy estimation between pairs of sequences of symbols, and then use classical classifiers (e.g., support vector machines) for text classification. Other applications of compression-based measures have been demonstrated by Pratas and colleagues, for genome analysis [ 17 , 18 ] or Carvalho et al for electro-cardiogram classification [ 19 ].…”

“…NRC has been used for applications such as authorship attribution [ 10 ], or studying the evolution of primate genomes [ 17 ]. The main advantage of NCD over NRC is that it can be evaluated using a common compressor, while the NRC requires a special-purpose one that is able to perform conditional compression.…”

“…However, the interesting difference comes from what they measure. NCD measures how two strings (files, images … ) are different in terms of the contents, while NRC of two strings attempts to answer on the portion of the second string that cannot be constructed from information of the first one [ 17 ]. With this in mind, it seems that both measures can be used for paper comparison, although the non-symmetry of NRC seems to be useful to determine the degree of novelty of a paper with respect to the other (provided that the differences in both directions vary), since it measures the amount of information that cannot be computed with the other.…”

Analisis Performa Rasio Kompresi Pada Metode Differensiasi ASCII Dan Lempel Ziv Welch (LZW)

“…Salah satu metode kompresi yang memiliki rasio kompresi yang cukup baik dan banyak digunakan saat ini adalah metode LZW. Metode LZW telah banyak digunakan pada beberapa penelitian perbandingan kompresi [4]- [11], [13], [16]. Sebagian hasil penelitian perbandingan menunjukkan LZW memiliki hasil rasio kompresi yang cukup baik sehingga pada penelitian ini juga akan digunakan sebagai pembanding terhadap metode kompresi differensiasi ASCII.…”

Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard

“…Should we also measure the information needed to describe the model selection? Recently, we answered these questions [ 39 ] using the Normalized Relative Compression (NRC) [ 41 , 42 ]. In fact, we showed that, if the models are not qualified to handle a specific region, then the information required to measure similarity is transferred to the selection of the used model.…”