Graphical and numerical representations of DNA sequences: statistical aspects of similarity

Abstract

New approaches aiming at a detailed similarity/dissimilarity analysis of DNA sequences are formulated. Several corrections that enrich the information which may be derived from the alignment methods are proposed. The corrections take into account the distributions along the sequences of the aligned bases (neglected in the standard alignment methods). As a consequence, different aspects of similarity, as for example asymmetry of the gene structure, may be studied either using new similarity measures associated with four-component spectral representation of the DNA sequences or using alignment methods with corrections introduced in this paper. The corrections to the alignment methods and the statistical distribution moment-based descriptors derived from the four-component spectral representation of the DNA sequences are applied to similarity/dissimilarity studies of β-globin gene across species. The studies are supplemented by detailed similarity studies for histones H1 and H4 coding sequences. The data are described according to the latest version of the EMBL database. The work is supplemented by a concise review of the state-of-art graphical representations of DNA sequences.

An Alignment-Free Algorithm in Comparing the Similarity of Protein Sequences Based on Pseudo-Markov Transition Probabilities among Amino Acids

“…The sequences have lengths 602~610 base pairs (bps). It is a popular benchmark data for testing the performances of computational methods in comparing the similarity of protein sequences [15, 31–34]. …”

Descriptors for DNA sequences based on joint diagonalization of their feature matrices from dinucleotide physicochemical properties

“…Thus, the descriptors could be derived from these matrices. These descriptors characterizing sequence can be used as the components of similarity measures between a pair of sequences [11] .…”

“…It is known that the four nucleic acids A, T, G, and C can be grouped A T G C A AA AT AG AC T TA TT TG TC G GA GT GG GC C According to Ref. [11], many different binary techniques have been assigned the values 0-1 to Y, K, S and to R, M, W, respectively. Considering graph theory, DNA/protein sequences may be regarded as node-edge-node models, where there are four types of nodes, A-T-G-C, and 16 kinds of edges (shown in Table 1).…”

“…Dual nucleotides may also be categorized into groups according to their physicochemical properties [11] (for reviews up to 2011).…”

Graphic Mapping of Protein-Coding DNA Sequence in Four-Dimensional Space and its Application

“…About the graphical methods visualizing DNA sequences, we can find more discussion in Randić's. 41 Recently, Bielińska-Wąż 42 gave a detailed review about graphical and numerical representations of DNA sequences. In addition, as for a type of alignmentfree method, some graphic methods for DNA sequence are also used to make genome comparison, such as Ref.…”