Prokaryotic Genome Annotation and Analysis

The J. Craig Venter Institute is offering a three-day course in Prokaryotic Genome Annotation and Analysis. This course will familiarize attendees with JCVI's prokaryotic annotation pipeline and manual annotation tool Manatee. It will also describe how to do analysis of the prokaryotic data on the Comprehensive Microbial Resource (CMR). At this class you will learn the searches, tools, and processes we use to annotate and analyze microbial genomes.

Upcoming Dates for the Course

April 15-17, 2008
June 10-12, 2008
August 5-7, 2008
October 14-16, 2008

Location

J. Craig Venter Institute
9712 Medical Center Drive, Rockville, MD 20850 (directions)

Course Details

In an effort to inform members of the research community about our annotation methods, to provide training for collaborators and other scientists who use our tools, and to inform the scientific public on the analyses available on the CMR, we have developed the Prokaryotic Annotation and Analysis course. Over 3 days (see details below), attendees are given detailed instruction on our annotation methods and tools and on the use of the CMR. By the end of the course you will:

Have learned all aspects of JCVI's prokaryotic annotation pipeline
Be able to evaluate our automated annotation and manually annotate prokaryotic genes
Have learned how to use our manual annotation tool Manatee
Have learned how to navigate and effectively use the Comprehensive Microbial Resource for comparative genomics

Day One

The first day of the course will focus on the annotation of prokaryotic genomes, including instruction on using JCVI's manual annotation tool called Manatee. Issues that will be covered include:

Gene Finding
Identification of potential Open Reading Frames using Interpolated Markov Models
Homology/Motif Searches
Blast-Extend-Repraze (BER), Hidden Markov Models (HMMs), TmHMM, SignalP, PROSITE, etc.
Identification of frameshifts, point mutations
Functional Assignment
Assignment of common names, role categories, gene symbols, Gene Ontology terms
ORF management
Start site curation, overlaps, and intergenics

Day Two

The morning of Day Two will involve hands on use of the manual annotation tool Manatee allowing users to put into practice the annotation information they were given on Day One.

The afternoon of Day Two will address the technical aspects of the data, including the storage of the data in a relational database and the installation of JCVI's manual annotation tool Manatee. Anyone interested in using Manatee locally at their own site should go to http://manatee.sourceforge.net/ to find out the requirements of the system and attempt to install it before coming it before coming to JCVI. On Day Two there will be time to address any issues you encountered installing Manatee.

Those who have submitted a genome to the JCVI Annotation Service (see below) at least one month before the start of the course will be able to start manually annotating their data on Day Two while at JCVI.

JCVI annotators will be available to assist with any annotation questions.

Day Three

The third day of the course will focus on how to navigate the CMR website and pull out meaningful information. The data generated at JCVI by the methods described above is available to the public through the CMR. We will go over all major aspects of the CMR including:

Genome Pages
Genome specific searches and results
Gene Pages
Specific attributes of a gene
Multi-Genome Pages
Searches and analysis across multiple genomes

The JCVI Annotation Service

To aid researchers sequencing and annotating prokaryotic genomes, we are offer the JCVI Annotation Service. This service has two components:

Output from JCVI's automated annotation pipeline
The open source manual annotation tool Manatee

The JCVI Annotation Service is offered completely free-of-charge. This service gives researchers outside of JCVI access to an already highly functional annotation pipeline and tool set, at no cost, saving these users huge amounts of time and money. To submit your genome please read the detailed description and submission guide.

Once you have read these two documents please fill out the submission form.

In order to have JCVI Annotation Service data ready in time for attendance at the Prokaryotic Annotation and Analysis course, you must submit the genome at least one month prior to the start of the course.

Submitting a genome is not required for this class, a test database can also be used during the class.

Manatee

Manatee is a freely available, open source tool which can be found at http://manatee.sourceforge.net.

Manatee allows viewing of search data and alteration of annotation in a user friendly, browser based format. It pulls information from an underlying database and associated files, displaying search results and current annotations. Annotators can then view the available evidence supporting the annotations and modify the annotations as needed.

If you are planning on installing Manatee you should attempt installation before coming to the class so any questions you might have can be answered when you get here. Installing Manatee is not necessary to attend the class.

Course Content Documentation

Files containing the content of the course materials distributed during the class are available here.

Registration

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

J. Craig Venter Institute
Training
9704 Medical Center Drive
Rockville, MD 20850

Fee: $595 includes all training materials and lunches for three days

Times: 9:30am to 4:30pm each day

Questions? E-mail us at training(AT)jcvi.org or call 301-795-7394.

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