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Comparative Genomics

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GMOD includes several components for managing and visualizing comparative genomics and synteny data.

Introduction

Comparative genomics and synteny are hot topics in biology and are frequently discussed at GMOD Meetings. GMOD offers several solutions for managing and visualizing comparative genomics data.

Presentations and Posters

GMOD Components

CMap

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

GBrowse_syn, as implemented at WormBase

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

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.

See the Sybil/IGS section of the Chado Comparative Schema page for how Sybil represents syntenic data in Chado.

SynView

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.