Primers4clades: A Web Server to Design Lineage-Specific PCR Primers for Gene-Targeted Metagenomics

Abstract

This chapter presents a practical overview and case study of the usage and capabilities of the primers4clades version 1.0 web server [Cont reras-Moreira et al., 2009], a software tool useful to desi gn degenerate PCR primers for gene-targeted analysis of metagenomic DNA (see also Chapter 28, Vol. I) and multilocus sequence analysis. Although direct shotgun sequencing of community DNA is now feasible [Venter et al., 2004], polymerase chain reaction (PCR) remains the most widely used technology to gain molecular markers for studies in molecular ecology and systematics.