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A hands-on Bioinformatics Workshop lead by Dr. Eric Lyons, University of California, Berkeley, USA will be held immediately prior to the SIP annual meeting.

8000 Genomes At Your Fingertips:

Comparative Genomics using CoGe

9 am – 4 pm Sunday, July 11, 2010

Trabzon, Turkey

“The best tool and presenter on the topic”
Dr. Volker Brendel, Bergdahl Professor of Bioinformatics, Iowa State University

Currently, there are genomes available for over 7500 organisms, with new ones being sequenced at an exponential rate.  New DNA sequencing technologies make obtaining genome sequences easier and faster, and modern researchers must understand genome biology in order to take advantage of this wealth of data.  CoGe, a web-based comparative genomics system, permits researchers anywhere in the world to easily analyze and compare genomes.  CoGe maintains a repository of all genomes publicly available, and its suite of interconnected analytical and visualization tools allows researchers to rapidly understand genome structure and evolution from the level of a gene to the genome.  This workshop lead by CoGe’s creator, Dr. Eric Lyons of the Department of Plant and Microbial Biology at UC Berkeley, USA, provides an introductory description of the structure, evolution, and dynamics of genomes that will be followed by a hands-on in silico training session using CoGe to characterize the structure and evolution of genomes. Workshop participants are encouraged to propose their invertebrate pathogens of interest for exploratory de novo research.

Specific topics will include:
1.    Producing an overview of a genome including GC DNA content bias, amino acid usage, codon usage
2.    Whole genome comparisons using syntenic dotplots
3.    Visualizing the differences in genome structure and evolution among the major domains of life
4.    Identifying ancient whole genome duplications, and regional inversions and rearrangements
5.    Gene duplications, translocations, deletions, and conserved non-coding sequences

Registration:

Participants should register for this workshop when they register for the SIP 2010 meeting. Seats are limited, so early registration is strongly encouraged. The fee for the workshop is 110 € for students and 170 € for others. The registration deadline is May 21, 2010. (Click for registration page)

Dr. Eric Lyons (Click for images) is based at UC Berkeley, USA. His current research is focused on understanding genome evolution and dynamics, genomics computational systems and advanced visualization of genomic data. He has over 10 years of academic and corporate genomics research experience, which lead to the development of the CoGe web-based comparative genomics system.  CoGe is being actively used by researchers all over the world, and CoGe workshops have been very enthusiastically received. Most importantly, Dr. Lyons began as an invertebrate pathologist, working on Autographa californica multiple nucleopolyhedrovirus with our very own Dr. Loy Volkman.
CoGe is publicly available at: http://synteny.cnr.berkeley.edu/CoGe

High resolution analysis of the complete genomes of the baculoviruses Anticarisa gemmatalis MNPV and Autographa california MNPV using CoGeʼs GEvo. (Click for images) Both genomes are ~130kb in length.  Each panel represents an entire baculovius genome with the dashed line in the middle separating the top and bottom strand of DNA. Gene models are represented as green arrows. Regions of sequence similarity as identified by BlastZ in the (++) and (+-) orientation are drawn above and below gene models respectively. Transparent colored wedges connect regions of sequence similarity and identify syntenic regions, inverted regions (many near the left side), and unique genes in each genome. These results can be regenerated at: http://tinyurl.com/ya7fowr

Syntenic dotplot of endosymbiont Wolbachia genomes from Drosophila melanogaster "(x-axis; 1.4 megabases)" and Drosophila simulans "(y-axis; 1.2 megabases)". (Click for images) Each axis is a linear representation of a genome.  A dot is drawn for every putative homologous gene pair between these genomes as identified by BlastN.  Syntenic regions are identified by collinear series of genes between these genomes using DAGChainer, and are colored green or red if there are in the same or opposite orientation respectively.  This plot shows extensive genome rearrangements between these genomes, probably from genomic inversions. These results can be regenerated at: http://tinyurl.com/yfe9fl9