Processing Biological Sequences in MATLAB

Abstract

matlab incorporates several bioinformatics functions packaged together in its Bioinformatics Toolbox. The Bioinformatics Toolbox provides functions for creating objects such as a biograph, the gene ontology, and trees for phylogenetic analysis. In addition, this toolbox provides several functions for downloading sequences from DNA, protein, and structure databases. Sequence analysis functions are provided for performing statistical analysis on the sequence data and for comparing DNA and protein sequences using the standard alignment methods (Needleman–Wunsch and Smith–Waterman) for global and local alignments. Capabilities for finding multiple sequence alignments, phylogenetic analysis, visualization, and modeling sequence profiles using Hidden Markov methods are included in the Bioinformatics Toolbox. The toolbox provides extensive functionality for retrieving, writing, and analyzing microarray data. The richness of tools included makes it possible to apply the concepts covered in the subsequent chapters within the framework of the same application. This chapter provides an overview of the basic functions that enable reading, writing, and displaying biological sequence data.