Selecting Prebuilt Comparisons
To view prebuilt comparisons between up to five genomic sequences, please
select the 'Pre-computed' tab from the menu.
Choosing the sequences to view involves a three step process:
- Select the sequences
- Select the region of the sequences to be displayed
- Optionally fine-tune viewing parameters, and view the comparison
a) Select the sequences
The first stage of the process involves selecting the sequences from the
WebACT database for which you wish to view a comparisons. A series of list
boxes will be displayed containing the available sequences. To limit the
length of the list boxs, initially only genome sequences are displayed. Above
the list boxes, you will find a tickbox which allows plasmid sequences to be added to the
Firstly, choose the number of sequences you wish to compare (default = 2),
up to a maximum of 5. On changing the number of sequences to be compared,
the web page will automatically update the form to provide the appropriate
number of genome lists. The sequences are listed by species name, and strain
(where available). The accession number of the sequence in the Genome
Reviews database is provided in brackets at the end of each selection.
Tip: After selecting a list box, start typing the name of the
species you require. The list box will try to select the species name you
Select the sequences of choice by highlighting the relevant entry in each
list and click ‘next’
b) Select region to display
Displaying the full genome comparisons
By default, the full length of each selected sequence will be displayed,
along with the relavent comparions. Viewing full comparisons can require
large volumes of data to be downloaded to your computer - up to 70 Mb for a
5 way comparison of 9 megabase genomes. It is therefore recommended to only
use this option if you have a fast network connection, and ample memory in
Alternatively, it is possible to view a particular region of the sequence.
there are two methods for selecting partial sequences for display: by gene
name or by selected genome region. It is possible to select the same region
on each sequence (i.e. bases 1 - 10000 of each sequence), or to define these
ranges individually (i.e. bases 1 - 10000 of sequence 1 and gene recA + 50 Kb
flanking sequence of sequence 2)
Setting the same range for each sequence
Selecting by gene name
This option allows you to view a region of defined size centred on a gene of
interest. Select ‘gene name’ and click the BROWSE button. This
launches a pop-up window with a drop-down listbox containing all the genes
that are present in each of the selected sequences.
Select the gene of interest from the drop-down list and click
‘select’. The gene name will appear in the main window. If
required, change the amount of flanking sequence on either side of the
selected gene that will be viewed (default 50,000 bp) and click
Should, there be multiple genes annotated with the same name in one
sequence, you will be presented with a list containing their positions
within the sequence and you may choose which copy you wish to view.
NOTE: Selecting sequences based on gene names is entirely dependant on the
gene being identified in the annotation of the sequences present in Genome
Selecting by region
This option allows you to choose the region of each genome to compare. For
example, you can select the first 100,000 bp of each selected genome (the
default). Note that in many cases this will give no or few hits due to
a lack of synteny etc. Any sequence range required can be entered using
this option, as long as the co-ordinates specified are within the bounds of
the sequences selected.
Set different range for each sequence
When selecting a different range, the three options above
(full sequence, by gene name, by region) will be displayed for each selected
sequence allowing you to specify the region to be displayed in each sequence.
When selecting by gene name, the 'browse' list you are now presented with contains
all genes annotated for that sequence only, allowing you to compare the
similarity of genes with different names.