Indexing before alignment

Indexing is an essential step in many bioinformatics applications, as it can greatly reduce the computational time and resources required for sequence alignment. It allows the alignment algorithm to quickly locate the query sequences in the reference genome, without having to search the entire genome for matches. In this section you will learn how indexing works.

Preprocessing

Indexing and k-mer indexes

Ordered structures for indexing

Hash tables for indexing

Practical: Implementing a k-mer index

Variations on k-mer indexes

Genome indexes used in research

Problem to solve

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1. Finding a Spliced Motif

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