Revision as of 23:55, 14 October 2009

GBrowse_syn is a synteny viewer based on GBrowse. This page describes how to configure GBrowse_syn.

Main Configuration File

Purpose

The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files and display options.

• This file ends with the extension ".synconf".

• An example of the config file for the WormBase synteny browser can be seen here.

Configurable Options

join

• Required setting
• The database source name (DSN) for the alignment database

#example
join        = dbi:mysql:database=pecan;host=localhost;user=nobody

source map

• Required setting
• This option maps the relationship between the species data sources, names and descriptions
• The value for "name" (the first column) is the symbolic name that gbrowse_syn users to identify each species.
• This value is also used in two other places in the gbrowse_syn configuration:

 1) it is used as the species name in the "examples" directive
 2) it is used as the species name in the .aln file

The value for "conf. file" is the basename of the corresponding gbrowse .conf files. This value is also used to identify the species configuration stanzas at the bottom of the configuration file.

# example:
#                 name         conf. file          description
source_map =     elegans      elegans_synteny     "C. elegans"
                 remanei      remanei_synteny     "C. remanei"
                 briggsae     briggsae_synteny    "C. briggsae"

tmpimages

• The URL for cached image and session data

# example
tmpimages   = /gbrowse/tmp

buttons

• The URL for stock GBrowse images, etc

# example
buttons       = /gbrowse/images/buttons

stylesheet

• default: /gbrowse/gbrowse.css
• The URL for the stylesheet

examples

• Example searches to show at the top of the page

#example
examples = elegans X:1050000..1150000
           elegans I:10762799..10789727
           briggsae chrX:620000..670000

zoom levels

• which zoom levels will be available in the navigation menu

zoom levels = 5000 10000 25000 50000 100000 200000 400000

config_extension

• default: 'syn';
• This specifies the extension of species-specific configuration files.
• If GBrowse_syn is used with stand-alone GBrowse data sources, change this option to 'conf'.
• To avoid confusing the configuration files parser, take care to select names for species-specific configuration files that are not similar to other file names. For example, do not use both elegans.conf (for GBrowse) and elegans.syn (for GBrowse_syn).
• NOTE: If you are using multiple data sources for gbrowse_syn, all must use the same config extension, you can not mix and match ".syn" and ".conf".

description

• default: none
• The description of the GBrowse_syn data source for public display

max_segment

• default: 400_000
• The maximum allowed segment size (sequence length) for the central reference panel
• Take care not to set this value too high. Very large segments may cause significant network latency or even time out the web server

max_span

• default: 0.3 (i.e., 30%)
• This is an advanced option.
• The maximum portion of the reference sequence size that will trigger merging of adjacent inset (aligned sequence) panels.

min_alignment_size

• default: 0.01
• The minimum alignment size, expressed as a fraction of the total reference sequence length, that will be used to create an inset panel.

imagewidth

• default: 800
• The width of the displayed sequence panels (pixels)

interimage_pad

• default: 5
• The space between inset panels (pixels)

vertical_pad

• default: 5
• The vertical space between panels (pixels)

align_height

• default: 6
• The height of the alignment syntenic block features (pixels)

max_gap

• default: 200_000
• This is an advanced option
• The maximum gap allowed between chained alignment features

overview_ratio

• default: 0.9
• The relative width of the overview panel in relation to the width of the detailed display panel

overview bgcolor

• default: gainsboro
• The background color of the overview panel
• Allowed values are named web colors or RGB hex codes (eg: '#FFFFFF')

The species' configuration stanzas

• Each individual species (or equivalent) that has a configuration files specified in the source map shouls also have a config stanza specifying which tracks to display and the theme color for the species.
• Note that the label of each stanza should map the second column in the source map.

[elegans_synteny]
tracks    = CG
color     = blue

[briggsae_synteny]
tracks    = CG
color     = purple

[remanei_synteny]
tracks    = CG
color     = black