engleski

Bioinformatics tools towards human genome analysis

The rapid progress in DNA sequencing technology will soon make the sequencing of the genomes of individuals commonplace. This will create the problem of analysing the mass of data to extract the relevant information. An integrated set of computer programs, the ClustScan (Cluster Scanner) suite of programs, was developed. ClustScan is an easy to use, rapid annotation tool that takes a top-down approach based on HMM models to annotate genes encoding biosynthetic enzymes forming metabolic pathways. The versatility of this program package has been demonstrated by annotating biochemical pathways in microbial, invertebrate animal and metagenomic datasets. The novelty of ClustScan over existing computer programs is the knowledge-based automatic prediction of activities and specificities of proteins under investigation. The open architecture of ClustScan allows easy integration with other programs, facilitating further analyses of results. The program is easily updated to incorporate new knowledge as well as standard format annotation files for DNA sequences. The analysis of an individual human genome requires a number of different sorts of analyses. This includes detection of mutations (both known and novel) that inactivate genes as well as determination of haplotypes that are linked to QTLs of medical and pharmacogenomic significance. The results of the analyses must be integrated with existing knowledge to produce a medically useful tool. Work is underway to extend ClustScan for comparative genome annotation to generate a novel tool for automatic genome annotation, TAGS (Tool for Analysis of Genome Sequences). We would welcome collaboration with clinicians in the development of TAGS.

human genome sequencing; comparative genome annotation; haplotypes; QTLs; computer program package; ClustScan; TAGS

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