Publications - Working papers
Please find below working papers of our group. Currently, we list 58 working papers.
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Genome Annotation without Genes
Jan Engelhardt, Toralf Kirsten, Peter F. Stadler, Sonja J. Prohaska
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Status: Submitted
GI 2010
Abstract
The concept of the gene plays a fundamental role both in the interpretation
and in the organization and storage of molecular biology data. Genes are
treated as if they were unambiguously characterized physical entities with
clearly defined measurable properties. The ubiquitous usage of genes in
current bio-databases reinforces this perception. A closer look at the
data models and the ongoing discussion of the gene concept itself, however,
exposes the gene as an ill-defined \emph{ad hoc} construct that is
unsuitable both as interface between functional annotation and sequence
level data and as organizing principle in molecular biology. It should thus be
abandoned in the context of genome annotation. As a collective of
associated DNA, RNA, and protein sequences, the gene should be replaced
with a more a more explicit model of the expression and processing cascade,
implying that functional annotation should be linked explicitly to physical
objects only.
Keywords
gene, genome annotation, ENSEMBL, RefSeq, OTTER