Some projects in our lab are websites as shown below.
MGIP - A system for multilocus sequence typing analysis.
The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing (MLST) data, at http://mgip.biology.gatech.edu. MLST is used to generate allelic profiles to characterize strains of Neisseria meningitidis, a major cause of bacterial meningitis worldwide. N. meningitidis strains are characterized with MLST as specific sequence types (ST) and clonal complexes (CC) based on the DNA sequences at defined loci. These data are vital to molecular epidemiology studies of N. meningitidis, including outbreak investigations and population biology. MGIP analyzes DNA sequence trace files, returns individual allele calls and characterizes the STs and CCs. MGIP represents a substantial advance over existing software in several respects: 1) ease of use - MGIP is user friendly, intuitive and thoroughly documented; 2) flexibility - because MGIP is a website, it is compatible with any computer with an internet connection, can be used from any geographic location, and there is no installation; 3) speed - MGIP takes approximately one minute to process a set of 96 trace files; and 4) expandability - MGIP has the potential to expand to more loci than those used in MLST and even to other bacterial species.
Neisseria Base - A genome browser for Neisseria spp.
The rate of genomes being completed is increasing exponentially, which places the bottleneck of genomic studies squarely on bioinformatics. Although there are central repositories such as GenBank for massive genomic data, there is a need for specialized resources. These resources already exist for some genera including Drosophila and Caenorhabditis. Fortunately these well-established databases are built on a genome browser platform Gbrowse. We are taking advantage of the platform for the creation of a Neisseria database called Neisseria Base. We have added many more capabilities, making Neisseria Base a rich resource for studying Neisseria species. In addition, we have completed four virulent N. meningitidis genomes (serogroups A,B,C, and W135) that we have sequenced using pyrosequencing technology. These genomes and the other existing completed Neisseria genomes will be made available on our browser for perusal and genomic analyses.