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Dr. Steven Wilhelm, Samantha Coy 2017. Using De-MetaST-BLAST. protocols.io dx.doi.org/10.17504/protocols.io.ii2ccgeCopy Citation Copied
URL: https://dx.doi.org/10.17504/protocols.io.ii2ccge
Authors: Dr. Steven Wilhelm, Samantha Coy
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Samantha R Coy's Protocols
Summary: Please contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol. De-MetaST-BLAST, written in C++, is a script that can validate degenerate primers by performing in silico PCR amplification of the primers against metagenomic and metatranscriptomic databases (e.g. CAMERA; MG-RAST). The output is a list of in-silco PCR amplicons that are then blasted against GenBank to determine the most homologous sequence to the amplicon. Modified from Gulvik, C. A., Effler, T. C., Wilhelm, S. W., & Buchan, A. (2012). De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes. PLoS ONE,7(11). doi:10.1371/journal.pone.0050362
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Version: 1
Publication Date: 2017
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Source: Protocols.io
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