Metagenomic ventures into outer sequence space

Dutilh, Bas E

The third reason that unknowns exist is methodological. Because the advances in DNA sequencing technology have greatly outpaced improvements in computer power, 20 bioinformatic approaches to analyze metagenomes often cut corners. For example, reference databases may be reduced to include only those references that are expected in the sample a priori. Moreover, read annotation may be limited to identifying almost exact sequence matches, as this can be computed much faster than if sequence variations needs to be taken into consideration in a permissive homology search. These issues lead to an inherent blind spot for discovering true novelty, such as sequences that are not expected in the sample, or organisms that have not been observed before. One way to, at least partially resolve this issue is by de novo assembly of the metagenome. Depending on the diversity of the sample, assembly can combine many short sequences (individual reads) into fewer, longer ones (assembled contigs). Reducing the number, and increasing the length of the sequences allows homology searches to be performed with more sensitive, computationally more expensive algorithms such as translated homology searches or profile searches, leading to more specific annotation and improved biological interpretation. Moreover, larger and more comprehensive reference databases can be used, allowing unexpected hits to be found.