De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes
Identifieur interne : 000515 ( Main/Exploration ); précédent : 000514; suivant : 000516De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes
Auteurs : Christopher A. Gulvik [États-Unis] ; T. Chad Effler [États-Unis] ; Steven W. Wilhelm [États-Unis] ; Alison Buchan [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
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 (
Url:
DOI: 10.1371/journal.pone.0050362
PubMed: 23189198
PubMed Central: 3506598
Affiliations:
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<front><div type="abstract" xml:lang="en"><p>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 (<italic>i.e.,</italic>
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 <italic>in silico</italic>
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 <italic>in silico</italic>
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 <italic>in silico</italic>
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, this search tool has potential utility in many data mining applications.</p>
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<affiliations><list><country><li>États-Unis</li>
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<region><li>Tennessee</li>
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<tree><country name="États-Unis"><region name="Tennessee"><name sortKey="Gulvik, Christopher A" sort="Gulvik, Christopher A" uniqKey="Gulvik C" first="Christopher A." last="Gulvik">Christopher A. Gulvik</name>
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<name sortKey="Wilhelm, Steven W" sort="Wilhelm, Steven W" uniqKey="Wilhelm S" first="Steven W." last="Wilhelm">Steven W. Wilhelm</name>
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