Several ways of visualizing the results of functional metagenomic analyses. The discussion is based on two studies focusing on the metagenomic analysis of the human distal gut microbiome.
Construct phylogenetic trees from mtDNA sequences for the Hominidae taxa (also known as pongidae). This family embraces the gorillas, chimpanzees, orangutans and humans.
Illustrates how to use the rnafold and rnaplot functions to predict and plot the secondary structure of an RNA sequence.
Calculate Ka/Ks ratios for eight genes in the H5N1 and H2N3 virus genomes, and perform a phylogenetic analysis on the HA gene from H5N1 virus isolated from chickens across Africa and Asia. For
How HMM profiles are used to characterize protein families. Profile analysis is a key tool in bioinformatics. The common pairwise comparison methods are usually not sensitive and specific
Illustrates a simple metagenomic analysis on a sample data set from the Sargasso Sea. It requires the taxonomy information included in the files gi_taxid_prot.dmp, names.dmp and
Illustrates a simple approach to searching for potential regulatory motifs in a set of co-expressed genomic sequences by identifying significantly over-represented ungapped words of
Generate bootstrap replicates of DNA sequences. The data generated by bootstrapping is used to estimate the confidence of the branches in a phylogenetic tree.
Use the Bioinformatics Toolbox™ to find potential primers that can be used for automated DNA sequencing.
An analysis of the origin and diffusion of the SARS epidemic. It is based on the discussion of viral phylogeny presented in Chapter 7 of "Introduction to Computational Genomics. A Case
How the analysis of synonymous and nonsynonymous mutations at the nucleotide level can suggest patterns of molecular adaptation in the genome of HIV-1. This example is based on the