Comparative Genomics

From GMOD
Revision as of 00:45, 16 February 2008 by Clements (Talk | contribs)

Jump to: navigation, search

GMOD supports synteny data with a number of components. This page describes and links to additional information for each of them.


Introduction

Comparative genomics and synteny are hot topics in biology and were frequently discussed at the November 2007 GMOD Meeting. GMOD offers several solutions to managing and displaying syntenic data.

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.

GMOD Synteny 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 and sequence assemblies. The package also includes tools for curating map data. Unlike the other tools listed here, it does not require sequence data.

See CMap for more.

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.

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

SynView

SynView is a GBrowse configuration file that creates a simple synteny viewer inside of GBrowse. SynView is included in the GBrowse distribution.

SynBrowse

SynBrowse is a generic sequence comparison tool for visualizing genome alignments both within and between species. It is intended to help scientists study and analyze synteny, homologous genes and other conserved elements between sequences. It is based on GBrowse.

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.