Computational tools and Interoperability in Comparative ... - CBS

Danmarks Tekniske Universitet AFI, Ph.d.-uddannelse
September 2005
Ph.d.-studerendes navn: Peter Fischer Hallin
Cpr.-nr.: 160877 2053
Studiets hovedemne:
The goal of this project is to obtain better understanding about the structural
mechanisms that are involved in the initiation of transcription of DNA in
Prokaryotic genomes and to use this information to make better and consistent
transcript predictions. We have presented a database (Hallin and Ussery 2004)
which holds several kinds of information for each of the over 300 fully
sequenced Prokaryotic genomes that are currently available. Different research
groups have made efforts to gather sequence data and analysis of the fully
sequenced microbial genomes that are being published.
Currently we rely on the authors' annotation of genome sequences when
comparative genomics are applied to our data sets. However, different authors
use different tools, approaches and criteria during the annotation process. There
are examples of genomes that are predicted to be 50-100% over annotated
(Skovgaard et al. 2001). Once reliable and automated processes for predicting
transcriptomes are established, comparative analysis can be applied on the entire
collection of organisms. It is envisioned that the users of our website can
interactively be able to browse any piece of DNA to look for structural properties
and repeats.
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Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A On the
total number of genes and their length distribution in complete
microbial genomes (2001) Trends Genet.17:425-8.
Peter F. Hallin and David W. Ussery CBS Genome Atlas
Database: A dynamic storage for bioinformatic results and
sequence data (2004). Bioinformatics 20:3682-3686.
(Her beskrives den videnskabelige projektdels indhold samt mål og midler. Hvis beskrivelsen er på mere end 1 A4side
gives en kort oversigt her med henvisning til selve beskrivelsen, der vedlægges som bilag).
Det eksterne
forskningsophold
Professor Craig John Benham, University of California, Davis.
Benhams research focuses on mathematical modelling of DNA
destabilization and prediction of opening of the DNA molecule
during a transcription event. His strong mathematical approach is
novel and would contribute significantly to our prediction methods
and could possibly help explaining biological / experimental
results. It is the idea that Craig Benhams calculations will be
integrated into the prediction algorithms that is a major topic of my
project.
A 12 weeks internship is scheduled for October-December to Craig
Benhams lab to integrate SIDD predictions (Stress Induced DNA
Duplex Destabilization) with CBS databases and to prepare 1-2
manuscripts on SIDD measures on a global prokaryotic scale.
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