An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges (original) (raw)

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Responsible for the Biodefense Division's sequencing and Comparative Analysis Group within the Biology and Biotechnology Research Program at the Lawrence Livermore National Laboratory, Livermore, California.

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Professor for Computer Science in the Center for Bioinformatics at the University of Hamburg, Germany.

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Professor for Theoretical Bioinformatics at the University of Ulm, Germany.

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Leads a Pathogen Bioinformatics team at the Lawrence Livermore National Laboratory.

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Received:

24 February 2003

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Patrick Chain, Stefan Kurtz, Enno Ohlebusch, Tom Slezak, An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges, Briefings in Bioinformatics, Volume 4, Issue 2, June 2003, Pages 105–123, https://doi.org/10.1093/bib/4.2.105
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Abstract

A team at the Lawrence Livermore National Laboratory (LLNL) was given the task of using computational tools to speed up the development of DNA diagnostics for pathogen detection. This work will be described in another paper in this issue (see pages 133–149). To achieve this goal it was necessary to understand the merits and limitations of the various available comparative genomics tools. A review of some recent tools for multisequence/genome alignment and substring comparison is presented, within the general framework of applicability to a large-scale application. We note that genome alignments are important for many things, only one of which is pathogen detection. Understanding gene function, gene regulation, gene networks, phylogenetic studies and other aspects of evolution all depend on accurate nucleic acid and protein sequence alignment. Selecting appropriate tools can make a large difference in the quality of results obtained and the effort required.

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© Henry Stewart Publications

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