Searching Gene and Protein Sequences for Domains and Motifs
The sequences of genes, proteins, and entire genomes hold clues to their function. Repeated subsequences or sequences with strong similarities to each other can be clues to things such as evolutionary conservation or functional relatedness. Sequence analysis for motifs and domains is a core technique in bioinformatics. Bioconductor contains many useful packages for analyzing genes, proteins, and genomes. In this chapter, you will learn how to use Bioconductor to analyze sequences for features of functional interest, such as de novo DNA motifs and known domains from widely used databases. You’ll learn about some packages for kernel-based machine learning to find protein sequence features. You will also learn about some large-scale alignment techniques for many sequences or very long sequences. You will use Bioconductor and other statistical learning packages.
In this chapter, we will cover the following recipes:
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