MPPOL GENEMAP: WEB BROWSER HELPER APPLICATION
IACR-Rothamsted, Harpenden, Herts AL5 2JQ, UK
Background and objectives
Molecular Plant Pathology On-Line (MPPOL) is an international peer-reviewed on-line journal edited and published by the British Society for Plant Pathology (BSPP). It publishes papers from all areas of molecular plant pathology, including research on diseases caused by fungi, viruses, nematodes, bacteria, insects, parasitic plants and other organisms. An important aspect of these papers is the sequence data that they publish. At present these are presented in text format in the HTML documents that make up MPPOL. The aim of this project was to develop helper application software (GeneMap) to display the sequence in graphical form, as a map, and to allow the reader/user to examine the map for sequence features discussed in the research paper.
Results and conclusions
GeneMap is a sequence display and analysis helper application for use with web browsers (e.g. Netscape and lnternet Explorer) on IBM PC-compatible computers running the Windows 3.1, Windows 95 and Windows NT operating systems. Once it has been installed and registered with the operating system and web browser, GeneMap is automatically launched when the web browser encounters sequence data in an HTML document. The sequence data are seamlessly downloaded from the web server and displayed within GeneMap. The data contain an enhanced feature table (EFT) which determines how GeneMap will display the sequence, e.g. as a linear or circular map, and contains information about various features that the author wants to display, e.g. restriction enzymes, primers, PCR fragments and ORFs. The EFT can be created by an author using GeneMap. The EFT does not simply store positional data for the features, it stores enzyme names, primer sequences, mismatch data, maximum PCR fragment lengths and minimum ORF lengths, etc. GeneMap knows the recognition sequences of >400 restriction enzymes, and uses the primer sequences and other data to analyse the target sequence to determine where the features are on the sequence. This is much more flexible, and allows the reader to use GeneMap to look for other restriction enzyme sites and to see where else the primers would bind if mismatches are allowed and what other PCR fragments might be generated. The reader can even see where his/her own primers might bind, or use the primers supplied on different sequences.
GeneMap enhances the ability of authors to display sequence data graphically from a web page. It also makes MPPOL papers more interactive for the readers, allowing them to use a sequence reported immediately without having to save it to a file, manually launch a separate analysis package, etc.
I am grateful to the BSPP Electronic Communication Committee for support, and especially Peter Scott and Adrian Newton for the help and encouragement given to this project.