Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 3/28/2010
Publication Date: 1/9/2011
Citation: Sparks, M., Li, R.W. 2011. Towards a more complete metagenomics toolkit. In: Li, R.W. editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 33-45.
Technical Abstract: The emerging scientific discipline of metagenomics has not only created a myriad of opportunities for biologists to reveal new insights into the microbial underpinnings of our environment, but has also presented a number of interesting challenges for bioinformatics algorithms and software developers. Some of the key areas for improvement comprise of sequence assembly, phylogenetic analysis, gene finding and data compression. Adaptation of techniques from the systems biology domain (e.g., approaches to gene network analysis) will be critical towards meaningful extraction of biological knowledge from metagenomic datasets. In this chapter, we conduct a survey of various bioinformatics tools currently available to research scientists, discuss some of their critical limitations and suggest directions in which important contributions to the field could be made by computer scientists.