Genomic Annotation

Thanks to a plethora of independent projects, maintained by universities and research institutions, nowadays genomic information is largely available in a number of public, freely accessible databases. On the other hand, the lack of universally recognized standards for data representation can make it difficult to select a definitive and unique source of information. In addition, these databases are not always interchangeable, since data from one source may be missing, incomplete, or simply different in the other, so that finding a one-to-one correspondence is sometimes impossible. To address these issues, the Genomic Annotation Manager has been developed, which aims to integrate heterogeneous data sources and provide a uniform and non-redundant knowledge base for genomic annotation. For instance, genes, mutations and SNPs (single-nucleotide polymorphisms) can be unambiguously identified by all modules within the LAS system. So far, sequence mutations from COSMIC: Catalogue of somatic mutations in cancer (http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/), and gene transcript information from the UCSC Genome Browser database (http://genome.ucsc.edu/) have been imported into the Genomic Annotation Manager. Furthermore, Blat (http://genome.ucsc.edu/cgi-bin/hgBlat) has been integrated to support different molecular experiments and annotation procedures.