Abstract

Genome sequencing provides a wealth of data which can be difficult to manually analyze and explore. The field of genome analysis also lacks many comprehensive graphically driven and intuitive tools for automated analysis of genome data. Here, I will discuss how to acquire, analyze, and interpret genomic data related to Paracoccidioides. The Broad Institute website (www.broadinstitute.org) hosts numerous genomic resources for Paracoccidioides and related dimorphic fungi, such as Histoplasma and Coccidioides, through the Fungal Genome Initiative. The website has data for available for download in a variety of formats, including nucleotide and protein sequences and genetic maps. I will discuss how access and read these different forms of data, with a focus on Paracoccidioides. I will then discuss downstream applications which can be used to process and explore this data, such as command line searching with BLAST and desktop genome visualization and exploration. Examples will be shown throughout. We will explore various analytical tools available on the Broad website, including 1) searching the Paracoccidioides genomes for genes of interest with BLAST and related tools, 2) exploring the genomes with functional queries, in order to identify groups of genes with related functions, and 3) methods to visually compare Paracoccidioides strains, including dot pots and synteny maps. Furthermore, I will discuss many of the analytical tools used in the analyses in the Paracoccidioides genome paper, with a focus on what kinds of questions can be answered using these tools. Some specific examples will include identifying gene families, functional classification of genes, and phylogenetic analysis. Finally, time will be available for discussing bioinformatic solutions to course member questions.