MOTIVATION: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Owing to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. RESULTS: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, operational taxonomic unit calling or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that ∼200 Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed. AVAILABILITY AND IMPLEMENTATION: Nonpareil is available at https://github.com/lmrodriguezr/nonpareil/ under the Artistic License 2.0.

Genome-scale metabolic reconstruction (GEMR), along with flux balance analysis, has been widely used to study complex metabolic networks in several microbial organisms. This approach is of particular applicability in biological systems where the lack of kinetics data is typical. This is the case of plant-pathogen interactions, where these methods open the possibility of studying host metabolic network phenotype during the interaction with pathogens. Since GEMRs are based on sequenced genomes, its applicability to organisms where genomic information is lacking is limited. Here we describe an alternative approach to GEMR: targeted metabolic reconstruction, where network reconstruction is guided by transcriptomic data instead of genomic information. This approach is being applied successfully in our laboratory for the Phytophthora infestans--Solanum tuberosum pathosystem.

Abstract Motivation: We developed a technique and a tool for degenerate primer design based on multiple local alignments employing the MEME algorithm supported with electronic PCR. The objective is to find adequate primers starting from sequences with poor global similarity. We show an example of its application in our laboratory to find sequences in Brachiaria with similarity to ESTs related to apomixis. Contact: [email protected]; [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

High-throughput techniques are somewhat restricted in developing countries. However, computational resources have evolved in recent years to become available to the general public, with greater ability to solve intense computational problems at low cost. Therefore, the vast amount of information that is currently being generated and the need for finding the underpinnings of several issues in biology, have been the impetus of the computational biology area in Latin America. Colombia is no exception, as its rich genetic diversity has convened the attention of several institutions, including both governmental and academic departments, to find how, where, and when these resources could be employed to its benefit. In this review, we introduce the efforts being made throughout the country to spread the word and establish a strong network from a mid- and long-term perspective.