Comparative Genomics

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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 were hot topics in biology and at the November 2007 GMOD Meeting. GMOD offers several solutions to managing and displaying syntenic data.


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

At the November 2007 GMOD Meeting Sheldon McKay presented GBrowse_Syn, a GBrowse-based prototype for displaying synteny data.

GBrowse_Syn is not yet released.