Computational tools and Interoperability in Comparative ... - CBS

Chapter 5
Conclusion and perspectives
Conclusion and perspectives
This thesis has presented a number comparative genomics tools that have been used
throughout different research projects and peer review publications. The aim has been to
provide methods that enable the scientist to keep up with the increasing speed by which
genome sequences are published. Visualization plays a key role and finding better ways
to present sequence information in a condensed and intuitive way is essential for deriving
knowledge from the large number of bacterial strains being sequenced.
Information content has previously been used to quantify conservation of DNA motifs,
and a recent extension of this information framework has allowed to model complete
promotors such as the P1/P2 system described in this work. The models shown here
are to a large extent specific towards E. coli P1/P2 sites. However, the design of the
matrix and spacing configuration format of the iscan tool enables for a much broader
application. The tool may be used to test different hypothesis of promotor configurations
across a broader range of organisms by estimating the promotor conservation a single
comparable measure. There is still efforts to be made to implement benchmarking and to
examine other promotor systems.
Since the start of the human genome project (HGP) in 1990 there has been large
investments to develop and improve sequencing technology. The present stage, where a
bacterial genome can be sequenced for a few thousand dollars within few hours, is a result
of years of competition and investments in genome projects. There are no signs that new
achievements in sequencing technology stops here. The concept of sequencing single DNA
molecules real time has long been an ultimate goal within genomics and DNA sequencing.
It has been demonstrated how a DNA synthesis reaction can be monitored real-time, by
immobilizing a DNA polymerase within a small (20 zeptoliter) well (Eid et al., 2009). If the
technology reaches a final product, it may well start a new era in comparative genomics.
Once it is possible to obtain a genome sequence at the same rate as the DNA replication
itself, and at superior read lengths, sophisticated software must be implemented for the
downstream processing. The technology can give a boost to the quality of metagenomic
sequencing, and solve the current issues of proper assembly of these data sets.
The BLASTatlas tool presented in this thesis incorporates a number of software to
calculate different DNA properties as well as scripts for mapping sequence alignments to a
reference genome. The number of dependencies makes it difficult to package the software
and make installation on other computer systems. To share these more complex tools
among scientists Web Services plays an important role and it has been demonstrated how
analysis and visualization methods can be offered using this technology. At first glance the
traditional web interfaces seems more user-friendly. However, implementing interoperable
methods like that of the BLASTatlas method, forces a process in which the communication
is formalized and defined in every detail. This allows direct integration into the user’s pro-
155