9.1. Diving In At The Deep End

The following example aims to display a variety of Jemboss features which can be followed immediately. Should you have little or no previous knowledge of Jemboss then please skip forward and return to this example, should you need to, once you reach the end of the chapter.

This chapter contains many practical activities for you to try. Macintosh users please read "click" for any "left click" directions and "ctrl and click" for any "right click" directions.

This example can be followed using either a remote Jemboss server, or a local installation and assumes that the Jemboss window has already been launched.

The following example aims to illustrate use of the Jemboss interface in the investigation of an enzyme involved in the anabolic pathway of lactose in the gram negative bacterium Escherichia coli.

In order to investigate some of the protein properties, the same sequence will be used in a variety of programs. The sequence list (Section, “Sequence Input”) enables the sequence to be selected as default by each program accessed.

Each time a new program is selected, the protein sequence for the Escherichia coli beta galactosidase enzyme will be automatically inserted into the input field.

This is the directory into which all files created in this example will be saved.

The pepinfo.1.png tab displays a variety of amino acid properties and suggests the protein is composed primarily of smaller aliphatic residues. The pepinfo.2.png tab displays three separate hydrophobicity plots and corroborates information on the first display by suggesting no large regions of hydrophobicity .

The above program extracts information on the features of the sequence directly from the Uniprot entry including secondary structural information and the location of the active sites which may be important for any mutation studies.

The search retrieves two sequences; one is for a beta-galactosidase 2 enzyme and will be removed.

Batch mode allows the analysis to run in the background so further analyses can be launched simultaneously if necessary. Results, however, may not be immediately obvious so an informative batch submission window will be displayed which you can configure to your taste.

This displays results in the EMBOSS default FASTA format which is not the best for identifying similarities in the alignment.