Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families.
Provides a fully automated pipeline for the design of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic lineages. Primers4clades implements an extended CODEHOP primer design strategy based on both DNA and protein multiple sequence alignments.
A web-based tool that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated.
Optimizes choice of polymerase chain reaction (PCR) primers. mopo16S is based on multi-objective optimization which performs: (1) improvement of the efficiency and specificity of target amplification; (2) maximization of coverage, in terms of the fraction of all bacterial 16S sequences from different species that are matched by at least one forward and one reverse primer from the set pair and (3) minimization of matching-bias, in terms of differences in the number of combinations of primers from the forward and reverse sets matching each bacterial 16S.
Automates the process of designing primers for high-resolution melting (HRM), fragment length polymorphism (FLP), and sequencing experiments. DesignSignatures also finds the best restriction enzyme to further diversify HRM or FLP signatures. This enables efficient comparison across many experimental designs in order to maximize signature diversity. DesignSignatures designs primers in three or four steps: (1) designing forward and reverse primers that will efficiently amplify as many input sequences (i.e., alleles) as possible; (2) determining the set of PCR products for each combination of forward and reverse primer; (3) scoring each candidate primer pair based on the diversity of its resulting amplicon signatures in sequencing, FLP, or HRM; (4) optionally, choosing the best restriction enzyme to further maximize signature diversity in FLP or HRM experiments.