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Each class can have a number of tags, which can point to various data types or cross-references to other objects. The presence or absence of some tags carry specific information. For example, the Gene class (Fig. 1) defines tags such as “Corresponding_CDS” and “Variation” to store references to the appropriate CDS and variation objects for a given gene. The “Live” tag has no subtags; its presence (or absence) indicates whether the gene is current (or has been retired). Individual tags can be accessed by name from instantiated objects, sparing programmers the tedium of complicated table joins typical of relational database systems.
Briggsae. For example, the lin-48 gene has a conserved expression pattern in C. elegans and C. briggsae, but the C. elegans upstream region contains two binding sites for the transcription factor EGL-38, whereas the C. briggsae promoter contains just one site (41). Furthermore, the C. elegans and C. briggsae EGL-38 binding sites have diverged in sequence, so that the C. briggsae site cannot compensate for mutations in the C. elegans sites. Comparison of the upstream regions of the C. elegans and C.
13, 2178–2189. 24. van Dongen, S. D. thesis. Graph clustering by flow simulation. Dutch National Research Institute for Mathematics and Computer Science, University of Utrecht. 25. Eisen, J. A. (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8, 163–167. 26. Ohno, S. (1970) Evolution by Gene Duplication. Springer Verlag, NY. 27. , Wolf, Y. , Koonin, E. , and Aravind, L. (2002) The role of lineage-specific gene family expansion in the evolution of eukaryotes.