Titlebook: Parasite Genomics Protocols; Sara E. Melville Book 2004 Humana Press 2004

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Annotation of Parasite Genomes,e correspondingly different depths of annotation depending on what methods are employed. Researchers using genome data should, therefore, understand how annotations are generated to assess their validity correctly and to determine what level of inferences can be made accordingly. Thorough annotation

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Oration

Expressed Sequence Tags, a single-pass sequence derived from a single complementary DNA (cDNA) clone, and the sequence serves to identify the gene from which it derives. We present a set of tested laboratory protocols for setting up and performing an EST analysis of any chosen species. These medium-throughput protocols do

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Expressed Sequence Tags,have significant internal redundancy. To facilitate analysis of small EST datasets from in-house projects, we present an integrated “pipeline” of tools that take EST data from sequence trace to database submission. These tools also can be used to provide clustering of ESTs into putative genes and to

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Positive Selection Scanning of Parasite DNA Sequences,tive mutations can provide a guide to biological processes that are potentially essential to the parasite. Random genetic mutations that confer selective advantage can act to alter amino acids so as to confer gain of function that has positive impact on the survival of the parasite. Directional sele

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Amplified (Restriction) Fragment Length Polymorphism (AFLP) Analysis,sity among various organisms with varying genomic complexity, from small bacterial to large plant genomes. AFLP analysis combines the reliability of restriction enzyme digestion with the utility of the polymerase chain reaction. The technique can be applied to studies of DNA of any origin and comple

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conception

Gene Expression Studies Using Self-Fabricated Parasite cDNA Microarrays,ns to study transcriptional processes in a systematic and high-throughput manner. Specifically in this chapter, we outline the ordered processes involved in large-scale parasite gene expression studies including complementary (cDNA) microarray fabrication, total RNA isolation, cDNA labeling using fl