de-metast-blast a tool for the validation of degenerate primer sets and data mining of publicly available metagenomesde-metast-blast简并引物的验证的工具集和数据挖掘的公开可用的基因组.pdfVIP

De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes 1 1,2 1 1 Christopher A. Gulvik , T. Chad Effler , Steven W. Wilhelm , Alison Buchan * 1 Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America, 2 Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America Abstract Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (i.e., degeneracies). Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an in silico amplification using user defined nucleotide sequence dataset(s) and primer sequences that may contain degenerate bases. The program returns an output file that contains the in silico amplicons. When De-MetaST is paired with NCBI’s BLAST (De-MetaST-BLAST), the program also returns the top 10 nr NCBI database hits for each recovered in silico amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases