User Manual

This document describes the second release of GenomeComp - a visualization tool for whole microbial genome comparison.

GenomeComp is a free software, you can redistribute it and/or modify it.

Contents

1. Introduction to GenomeComp
1.1 What is GenomeComp?
1.2 System Requirements
1.3 Getting and Installing GenomeComp
1.3.1 Installation Instructions for Unix/Linux
1.3.2 Installation Instructions for Mac OS X
1.3.3 Installation Instructions for Windows

2. Starting GenomeComp
2.1 Running GenomeComp
2.2 Configuration Window
2.3 Main Window
2.3.1 Overview
2.3.1.1 Color representation
2.3.1.2 Fixed length and color
2.3.1.3 Miscellaneous
2.3.1.3.1 Figure scale
2.3.1.3.2 Length filter
2.3.1.3.3 Island color
2.3.1.3.4 ORFs color
2.3.2 The File Menu
2.3.2.1 Reset
2.3.2.2 Start
2.3.2.3 Save setting
2.3.2.4 Load DEFAULT
2.3.2.5 Save
2.3.2.6 Exit
2.3.3 The Options Menu
2.3.3.1 Configure
2.3.3.2 Compare type
2.3.3.2.1 Self-compare
2.3.3.2.2 Two sequences
2.3.3.2.3 Three sequences
2.3.3.3 Input format
2.3.3.3.1 Fasta format sequence
2.3.3.3.2 Genbank format sequence
2.3.3.3.3 EMBL format sequence
2.3.3.3.4 BLAST output file
2.3.3.4 Anchor style
2.3.3.4.1 Left
2.3.3.4.2 Center
2.3.3.4.3 Right
2.3.3.4.4 Custom
2.3.4 The Search Menu
2.3.4.1 Find ORF
2.3.4.2 Find Next
2.3.4.3 Go to Position
2.3.5 The List Menu
2.3.5.1 Length setting
2.3.5.1.1 All length
2.3.5.1.2 Above 50 bp
2.3.5.1.3 Above 1 Kbp
2.3.5.1.4 Above 5Kbp
2.3.5.1.5 Custom
2.3.5.2 Specific regions
2.3.6 The Hide Menu
2.3.6.1 Nothing
2.3.6.2 Control panel (left)
2.3.6.3 Display panel (right)
2.3.7 The View Menu
2.3.7.1 Title
2.3.7.2 ORFs
2.3.7.3 ORFs text
2.3.7.4 Ruler
2.3.7.5 Ruler text
2.3.7.6 Island bar
2.3.8 The Help Menu
2.3.8.1 Topic
2.3.8.2 About
2.4 Some Pop-up Windows
2.4.1 Confirm sequence name and length, Select program and parameters Window
2.4.2 The Detail Information Window
2.4.3 Specific regions list Window
2.4.4 The Save Window

3. Examples for Using GenomeComp
3.1 Two Sequences Comparison (a step-by-step tutorial)
3.2 Three Sequences Comparison

4. GenomeComp tips and tricks
4.1 Customize the colors in the canvas
4.2 Zoom the display of comparison
4.3 Limit the range of matches
4.4 Skip the BLAST comparison process
4.5 Enlarge your eyeshot of the canvas
4.6 Remove items from the canvas

5. Getting Help or Bug Report