Plant, Animal & Microbe Genomes X Conference Plant, Animal & Microbe Genomes X ConferenceJanuary 12-16, 2002
Town & Country Convention Center
San Diego, CA
Bioinformatics: Software
A physical map of the wheat D genome will be constructed using the diploid species, Aegilops tauschii, which was the donor of the D genome in the NSF project of Assessment of the insular organization of the wheat D genome by physical mapping. All the data, contig maps, physical maps, and project information including project summary, full description, progress, participants, and some useful links for this project, can be accessed through the project web site http://wheat.pw.usda.gov/PhysicalMapping. FPC software from Sanger Center, UK is used to assembly contigs. FPC is an interactive program for building contigs from fingerprinted clones for large scale sequencing projects, which can create contig maps with associated markers and then output to a fpc file (*.fpc). The contig maps and related data can be viewed through FPC software under Unix/Linux systems. To display contig maps, related data of fingerprinted clones, and associated markers on the web, a FPC Web Viewer was designed and developed. FPC Web Viewer is a client-server-database system to interactively display all contig maps and clones with associated markers for multiple FPC databases on the Web and connect to wEST and GeneBank databases. The relational-object database system PostgreSQL is adopted to store the data of clones, markers, and contigs. A utility Java program FPC Data Manager was developed to convert FPC flat data (*.fpc) from FPC software, *.bands, *.gel and *.sizes from Image program (Sanger Center, UK) into relational databases, to manage FPC databases, and to submit data to other public databases (wEST, GeneBank). Java technology (servlets and applets) , perl and HTML are used to develop the application server and clients. FPC Web Viewer is accessible through web page http://wheat.pw.usda.gov/PhysicalMapping/contigmaps.html. The contig maps of D genome FPC database and seven databases from other physical mapping projects ( rice, maize, arabidopsis, sorghum, mouse and human) can be viewed through FPC Web Viewer.