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A semi-automated approach to the representation of genetic maps

Alex Nip
Lin Liu
Charbel Seif
Nicolas Brossard
Gertraud Burger
Franz B. Lang
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Alex Nip

Résumé du colloque

Genomic data are typically presented in literature and scientific meetings in the form of genetic maps, as they permit gene contents and organization, information density and genome rearrangements to be visualized and features across different genomes to be compared with ease. However, preparing high-quality genetic maps is a time-consuming and tedious process. This is particularly true for genomes which consist of heavy clusters of closely spaced coding regions or introns, as their corresponding genetic labels tend to overlap severely. The conventional approach often requires using an interactive graphic package to construct each label painstakingly and to assign standardized attributes to various sections of the map. The creation of each such genetic map demands many hours of manual labor. With the rapid progress in DNA sequencing technology, an increasing number of data set on complete genomes are being generated at an unprecedented rate. Consequently, preparing a large number of genetic maps has become a challenge especially to comparative genomics research endavours such as the Organelle Genome Megasequencing Program (OGMP) whose mission is to generate a taxonomically broad collection of complete genome sequences from mitochondria and chloroplasts. With a set of about 100 complete mitochondrial DNA sequences (16-200 kbp) and about 15 complete chloroplast DNA sequences (120-200 kbp), informatic tools to assist map creation are urgently needed. In response, we have developed a semi-automated system which uses 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 high-quality Postscript output which can be further embedded in other word-processing documents. The focus of this talk is directed towards these two principle components. GMDL is introduced and discussed in detail. The translator's key algorithm, which is responsible for identifying and resolving overlapping genetic labels, is also presented.

Contexte

Section :
Biologie informatique
news icon Thème du colloque :
Biologie informatique
manager icon Responsables :
Nadia El-Mabrouk
host icon Hôte : Université de Montréal

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Thème du colloque :

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A semi-automated approach to the representation of genetic maps
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A semi-automated approach to the representation of genetic maps
Alex Nip
A semi-automated approach to the representation of genetic maps
Alex Nip