GMOD includes several components for managing and visualizing comparative genomics and synteny data.
Presentations and Posters
- GMOD Tools for Comparative Genomics - Poster about the tools described on this page.
- Modeling and Displaying Synteny w/ SynView - presented by Steve Fischer at the November 2007 GMOD Meeting, is a good overview of many issues encountered when displaying synteny.
- An Example Comparative Genome Database for Yeasts Using GMOD Tools - poster by Scott Cain showing how six GMOD tools are used to create an example comparative genome model organism database.
- Comparative Genomics With GMOD and BioPerl - a 2004 presentation by Jason Stajich.
CMap is a web-based tool that allows users to view comparisons of a wide variety of data including genetic maps, physical maps, sequence assemblies, QTL and deletion maps. Unlike the other tools listed here, it does not require sequence data.
CMap can display correspondences between features such as markers, HSPs or any other annotation. The distribution comes with tools for creating these correspondences based on feature names or correspondences can be imported directly. CMap can display correspondences as either lines or ribbons.
See CMap for more.
GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It can be used to view multiple sequence alignment data, synteny or co-linearity data from other sources against genome annotations provided by GBrowse. GBrowse_syn is included with the standard GBrowse package (version 1.69 and later). Working examples can be seen at TAIR, WormBase, and SGN.
Sybil is a web-based system for comparative genomics visualizations. It is currently developed by engineers at JCVI and at IGS at the University of Maryland School of Medicine. Sybil supports several visualizations: Whole genome comparisons, regional comparisons (synteny) and orthologous gene comparisons.
SynBrowse is a generic sequence comparison tool for visualizing genome alignments both within and between species. SynBrowse displays synteny based on nucleotide or protein alignment. It uses color intensity to indicate degree of similarity. SynBrowse is built on several open source packages, including parts of GBrowse, resulting in a similar look and feel.
SynView displays synteny at the region and/or gene level. Users select a reference genome and then synteny with other selected genomes is displayed relative to that genome. SynView is based on GBrowse. It can be layered on top of an existing GBrowse instance and uses the full range of GBrowse's display and configuration options. SynView is included in the GBrowse distribution.