Eukaryotic Genome Annotation and Analysis Course

The J. Craig Venter Institute is offering a three-day course in Eukaryotic Annotation and Analysis. This course will familiarize attendees with JCVI's eukaryotic annotation methods, tools and computational pipeline for annotation, including our manual annotation tool, Manatee. In this class you will learn about many of the searches, tools, and processes we use to annotate, analyze and compare eukaryotic genomes. You will learn how to put together an analysis "pipeline" for the annotation of a genomic sequence, and how to determine structural and functional characteristics of the features (repeats, genes and gene products, RNAs, etc). You will have the opportunity to use real data to practice with some of the tools we use for structural and functional annotation and comparative analysis. You will also gain a deeper understanding of the annotations available in publicly accessible databases.

Upcoming Dates for the Course

April 1-3, 2009
June 10-12, 2009
September 23-25, 2009

Location

J. Craig Venter Institute
9704 Medical Center Drive, Rockville, MD 20850 (directions)

Course Details

As more eukaryotic genomes are sequenced, the need for high quality, consistent annotation is greater than ever. The annotation that describes the features of a genome is a vital complement to the data produced by any genome sequencing project. In general, annotation includes the identification of features in the genome sequence, such as genes, regulatory elements and repeats. It usually includes identification of attributes such as functional name, protein domains, protein family membership, Enzyme Commission (EC) number and Gene Ontology terms to features like proteins and RNAs. The task of predicting the functions of newly identified proteins is complex and requires the integration of diverse sources of information. This course will inform you in the following topics.

Day One

The first day of the course will focus on the structural annotation or identification of and correct modeling of sequence features, including instruction on using open-source tools to evaluate the structural annotation of genes. We will cover the entire eukaryotic structural annotation pipeline including the discovery of repeats and identification of genes and other features, using publicly available software. We will discuss types of gene-finding algorithms, cDNA and EST based refinement, and combining multiple types of evidence to a single consensus prediction. In the hands-on session in the afternoon, you will have the opportunity to use software to critically evaluate the gene structures, including start and stop codons and exon/intron structure.

Day Two

On Day 2, we will present the functional annotation methods and tools we use to identify features of RNAs, genes and gene products. You will learn about various homology and motif searches, including signal sequences and localization motifs. We will discuss strategies and methods for assigning names accurately, and demonstrate ways of predicting Gene Ontology terms, protein family membership and metabolic pathway information. In the afternoon, you will use publicly available tools to put into practice the functional annotation methods covered that morning.

Day Three

The third day of the course will focus on comparative genome analysis and whole-genome alignment. You will learn how to navigate through a comparative analysis using open-source tools such as MUMmer and the Artemis Comparative Tool. You will be introduced to the TIGR Sybil interface which allows you to view and analyze the protein clusters in a comparative analysis.

For further clarification of content, e-mail lhannick(AT)jcvi.org or call 301-795-7857.

Registration

Registration forms can be emailed to training(AT)jcvi.org, faxed to 301-795-7055, or mailed to:

J. Craig Venter Institute
Training
9712 Medical Center Drive
Rockville, MD 20850

Fee: $695 includes all training materials and lunches for three days

Times: 9:30am to 5:00pm each day

General questions: training(AT)jcvi.org or call 301-795-7394.

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