MAPIT

MAPIT -- a semi-automated approach to the representation of genetic maps. Genomic data is typically presented in the form of genetic maps, as they permit visualization of gene content and organization, genome information density and rearrangements, as well as comparison of genome features across different organisms. However, preparing high-quality genetic maps is a time-consuming and tedious process and has become a challenge, especially to research endeavors in comparative organelle genomics involving the generation of a taxonomically broad collection of complete genome sequences from mitochondria and chloroplasts. With a set of more than 100 complete mitochondria and about 15 complete chloroplast DNA sequences (6 -- 200 kbp), informatics tools to assist map creation are urgently needed. In response, we have developed a semi-automated system, MAPIT, including a specially designed Genetic Map Description Language (GMDL), and an “intelligent” Postscript translator. While the former provides a way to customize and assign detailed attributes to each map element, the latter translates the map description into a Postscript output which can be further processed by standard graphical art software. We will describe here GMDL as well as the key algorithm of the Postscript translator, which is responsible for identifying and resolving overlapping genetic labels.