An introduction to MGIP
The Meningococcus Genome Informatics Platform (MGIP
) is a group of computational tools for the analysis of multilocus sequence typing (MLST
) data. MLST
is used to generate allelic profiles to characterize strains of Neisseria meningitidis
, a major cause of bacterial meningitis world-wide, as specific sequence types (ST
) and clonal complexes (CC
) based on the DNA sequence of defined regions of a specific set of housekeeping genes. These data are vital to global epidemiology as they provide information on the population biology of N. meningitidis
analyzes ABI sequence trace files, returns individual allele calls and characterizes the ST
s and CC
s. Previously, the only standard software for analyzing MLST
data was STARS, a software package which runs solely on Linux machines and is thus not available for many labs, particularly those in the developing world. MGIP
represents a substantial software advance in several respects: 1) speed
takes only one minute to process a set of traces while STARS may take up to 20 minutes, 2) ease of use
is user friendly, intuitive and thoroughly documented, 3) 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, and 4) expandability
has the potential to expand to more loci than those used in MLST
and even to other bacterial pathogens. Currently MGIP
has the capacity to analyze more than 15 loci.
For input, MGIP takes ABI sequence trace files and a mapping spreadsheet that indicates the strain, locus origin and orientation of each trace. For each trace, MGIP makes base calls, which the user can edit, assembles complementary sequence reads and compares assembled sequences to a database of alleles. Allele calls are then made for the individual loci. For each individual strain/locus combination, the MGIP output consists of 1) the allele call, 2) the BLAST results leading to the allele call, 3) the consensus sequence and quality scores from the complementary reads, 4) the aligned trace files from the complementary reads, and 5) the ST and CC designations determined using the allelic profile of the loci used for MLST. In addition, all of the files underlying each step in the analysis are available for download. Final results of the MLST analysis are viewable as a strain table and can be downloaded as a spreadsheet.
Please see the about page for more background information or continue reading for how to use MGIP.