Sequencing Strategies for Parasite Genomes -- Annotation of Parasite Genomes -- Parasite Genome Databases and Web-Based Resources -- Expressed Sequence Tags -- Expressed Sequence Tags -- Positive Selection Scanning of Parasite DNA Sequences -- RACE and RAGE Cloning in Parasitic Microbial Eukaryotes -- Amplified (Restriction) Fragment Length Polymorphism (AFLP) Analysis -- Minisatellites and MVR-PCR for the Individual Identification of Parasite Isolates -- Analysis of Differentially Expressed Parasite Genes and Proteins Using Transcriptomics and Proteomics -- Gene Expression Studies Using Self-Fabricated Parasite cDNA Microarrays -- DNA Content Analysis on Microarrays -- Typing Single-Nucleotide Polymorphisms in Toxoplasma gondii by Allele-Specific Primer Extension and Microarray Detection -- Transfection of the Human Malaria Parasite Plasmodium falciparum -- A PCR-Based Method for Gene Deletion and Protein Tagging in Trypanosoma brucei -- Analysis of Gene Function in Trypanosoma brucei Using RNA Interference -- In Vitro Shuttle Mutagenesis Using Engineered Mariner Transposons -- Random Mutagenesis Strategies for Construction of Large and Diverse Clone Libraries of Mutated DNA Fragments -- Separation, Digestion, and Cloning of Intact Parasite Chromosomes Embedded in Agarose -- Chromosome Fragmentation in Leishmania -- FISH Mapping for Helminth Genome -- Fiber-FISH: Fluorescence In Situ Hybridization on Stretched DNA -- Yeast Two-Hybrid Assay for Studying Protein-Protein Interactions -- From Genomes to Vaccines for Leishmaniasis.

Parasitic disease remains an important health issue in most regions of the world and constitutes a major cause of morbidity and mortality in developing countries. In Parasite Genomics Protocols, pioneering bench researchers describe in detail the cutting-edge techniques they have developed for analyzing the genomes and gene products in a diverse range of protozoan and metazoan parasites. These readily reproducible techniques can be used in genomic, functional genomic, and postgenomic studies and include transfection methods and vectors for several protozoan parasites, global analysis using microarrays, gene ablation using RNA interference, gene knockout, mutagenesis, and chromosome manipulation. Some of the protocols require DNA sequence data, whereas others were developed independently of whole-genome sequence data. Additional chapters survey the available genome sequences, helping novice researchers overcome the difficulties of accessing the databases and applying bioinformatics analysis to biological function. The protocols presented follow the successful Methods in Molecular Biology™ series format, each one offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of equipment and reagents, and tips on troubleshooting and the avoidance of known pitfalls. State-of-the-art and highly practical, Parasite Genomics Protocols offers bench investigators in parasitology a wide-ranging collection of diverse methods for elucidating the content of the genomes of parasitic organisms, utilizing the genome sequence for genetic analysis, and ascribing function to the available genome sequences.