GMOD

GBrowse syn Tutorial 2010

Further Reading

A Note on Whole Genome Alignments

The focus of the section of the course is on dealing with alignment or synteny data and using GBrowse_syn. However, how to generate whole genome alignments, identify orthologous regions, etc, are the subject of considerable interest, so some background reading is listed below:

• Primer on Hierarchical Genome Alignment Strategies
• article on PECAN and ENREDO
• all about PECAN
• The gene annotations for each species are in GFF files.
• The alignment data are in a constrained CLUSTALW format (They were not generated by the program CLUSTALW, which is not necessarily suitable for whole genome alignments)
• There are processing steps for the alignment data but it is very computationally intensive and we will load pre-processed data to get a head start.

Documentation

There is detailed documentation on the GMOD wiki for how to install, configure and use GBrowse_syn. To get started, browse these pages:

• GBrowse_syn overview
• Installation
• Configuration
• Alignment Data
• The user interface
• Presentations and workshops

Categories:

• GBrowse syn
• Tutorials

Navigation menu

Navigation

• GMOD Home
• Software
• Categories / Tags

Documentation

• Overview
• FAQs
• HOWTOs
• Glossary

Community

• GMOD News
• Training / Outreach
• Support
• GMOD Promotion
• Meetings
• Calendar

Tools

• Browse properties

• Last updated at 11:43 on 9 January 2013.
• Content is available under a GNU Free Documentation License unless otherwise noted.