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Alignment and Mapping

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Phylogenomics

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Abstract

Alignments represent hypotheses of positional homologies between nucleotides or amino acids of sequences. Global alignments infer positional homology across all sites of aligned sequences, whereas for local alignments positional homology is only optimized for substrings of sequences. Pairwise alignments of sequences can contain matches, mismatches and gaps, which can be used to define scoring functions to compare the quality of any two pairwise alignments. A solution for finding the optimal global pairwise alignment is the Needleman and Wunsch algorithm, which consists of matrix initialization, matrix filling and traceback. Local alignments are used to find similarities (and putative homologies) between two sequences, as used in database searches. Optimal local alignments are recovered by the Smith and Waterman algorithm. Faster database searches can be conducted using BLAST, a local alignment tool based on a seed-and-extend approach. Heuristic approaches are used to conduct multiple alignments. Most popular are progressive alignments, which use a series of pairwise alignment operations and a phylogenetic guide tree to construct the multiple sequence alignment. Masking and exclusion of unreliably aligned positions of sequence alignments can be used to improve the signal-to-noise ratio of the data. Noisy alignment positions can be inferred by identifying conserved blocks, using model-based approaches, or by investigating the consistency of alignments with respect to its used parameters. A specific alignment problem is the mapping of sequence reads to reference sequences. Most mapping algorithms are either based on a seed-and-extend approach or methods related to the Burrows-Wheeler transform, which is more memory efficient and less time-consuming. Specific mapping approaches exist to recover splice junctions or to recover methylation patterns. Finally, whole genomes can be aligned using methods broadly classified into hierarchical and local approaches, to recover syntenic regions across genomes.

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  1. Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), Madrid, Spain

    Christoph Bleidorn

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Bleidorn, C. (2017). Alignment and Mapping. In: Phylogenomics. Springer, Cham. https://doi.org/10.1007/978-3-319-54064-1_6

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