Jemboss Alignment Editor
Keywords: java, biology, bioinformatics, EMBOSS, GUI, Jemboss, alignment, computational biology, sequence analysis, interface, alignment

# Jemboss DNA Editor

This is a beta release of a graphical DNA editor which can be downloaded independently of the main Jemboss interface from the web-site above. It can be used to generate publication quality images of linear and circular DNA maps to display regions and features of interest. The images can be inserted into a document or printed out directly.

Currently EMBOSS has two programs, 'lindna' and 'cirdna', to draw linear and circular DNA respectively. These require input files, which describe the names and positions of the genetic markers. In these files the user also enters data for controlling the appearance of the markers. There are a number of advantages to the new Jemboss DNA editor. For example, there is no need for the user to create input files. Creating and editing the DNA map is all done graphically. This means the features are instantly shown when added by the user. It is also not restricted to a computer platform and can run on unix, Windows, MacOSX. The editor will read in the input files used by the EMBOSS programs ('lindna' and 'cirdna') and write them out.

A DNA map, for example, can be simply constructed using the graphical 'DNA Design Wizard' tool. This allows genetic markers to be defined and displayed with labels (e.g. ORF, CDS) and different colour. Exons can also be represented with arrows. Restriction enzyme sites can also be clearly marked and identified using colours and labels. Alternatively an existing input file for the EMBOSS application 'cirdna' can be opened directly from the file menu. The colour and position of all these features can be edited or saved to a file.

The Jemboss DNA editor is designed to be extensible. So, future plans for this include integration with Jemboss and the ability to read in and display features from sequence feature tables.