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Alignment-free sequence analysis
The emergence and need for the analysis of different types of data generated through biological research has given rise to the field of bioinformatics. Molecular sequence and structure data of DNA, RNA and proteins, gene expression profiles or micro array data, metabolic pathway data are some of the major types of data being analysed in bioinformatics. Among them sequence data is increasing at the exponential rate due to advent of next-generation sequencing technologies. Since the origin of bioinformatics, sequence analysis has remained the major area of research with wide range of applications in database searching, genome annotation, comparative genomics, molecular phylogeny and gene prediction. The pioneering approaches for sequence analysis were based on sequence alignment either global or local, pairwise or multiple sequence alignment. Alignment-based approaches generally give excellent results when the sequences under study are closely related and can be reliably aligned, but when the sequences are divergent, a reliable alignment cannot be obtained and hence the applications of sequence alignment are limited. Another limitation of alignment-based approaches is their computational complexity and are time-consuming and thus, are limited when dealing with large-scale sequence data. The advent of next generation sequencing technologies has resulted in generation of voluminous sequencing data. The size of this sequence data poses challenges on alignment-based algorithms in their assembly, annotation and comparative studies. Thus, alignment-free sequence analysis approaches provide attractive alternatives over alignment-based approaches.
== Alignment-free methods ==
Alignment-free methods can broadly be classified into four categories: a) methods based on k-mer/word frequency, b) methods based on substrings, c) methods based on information theory and d) methods based on graphical representation. Alignment-free approaches have been used in sequence similarity searches, clustering and classification of sequences, and more recently in phylogenetics (Figure 1).
Such molecular phylogeny analyses employing alignment-free approaches are said to be part of ''next-generation phylogenomics''.〔 A number of review articles provide in-depth review of alignment-free methods in sequence analysis.
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