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 list.

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 type

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 your computer.

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 ‘next’.

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 Reviews.

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.