ACeDB is a database of genome mapping information for the nematode worm Caenorhabditis elegans. It is accessed through an object-oriented graphical user interface which is also used by the Arabidopsis thaliana (AAtDB), the human chromosome 21, the grain genes and the Mycobacterium databases.
ACeDB is a large program and the following exercises only demonstrate its basic features. However, the graphical nature of the program makes it easy to explore and experiment with. In addition, extensive help is available on-line at every step.
A complete mapping project brings together genetic mapping (the process of locating the genes responsible for given phenotypes, for example using recombination data) and the physical mapping of restriction enzyme sites. ACeDB allows the retrieval of these data at various levels, from whole chromosomes down to individual genes. This includes information about alleles, genetic loci, clones, contigs (assemblies of overlapping clones), sequences and much more. Each particular item of information is classified according to its type (e.g. chromosome, allele, author, journal, clone, gene etc.). Related items of information are linked together, so it is possible, for example, starting from a given gene, to retrieve the information available about its physical mapping, its genetic map location, its various alleles, the DNA clone on which it was mapped, the journal article describing it, the authors of this article, the laboratory they worked in and so on.
Note: the basic ACeDB software is easily adapted to store all kinds of information pertaining to genome mapping. For example, AAtDB (the Arabidopsis thaliana database) contains digitized photographs of various Arabidopsis mutants and of autoradiograms, which can be viewed on the screen using a graphical display program called xv.
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