De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes
| Autor: | Steven W. Wilhelm, T. Chad Effler, Alison Buchan, Christopher A. Gulvik |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Sequence analysis
In silico Science Gene Identification and Analysis User defined Biological Data Management Biology computer.software_genre Microbiology Microbial Ecology Molecular Genetics 03 medical and health sciences Engineering Genome Analysis Tools Degenerate primer Data Mining 030304 developmental biology DNA Primers 0303 health sciences Internet Multidisciplinary 030306 microbiology Nucleic acid sequence Computational Biology Genomics Amplicon Metagenomics Signal Processing Metagenome Medicine Data mining Primer (molecular biology) Databases Nucleic Acid computer Sequence Analysis Software Research Article |
| Zdroj: | PLoS ONE, Vol 7, Iss 11, p e50362 (2012) PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | 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, this search tool has potential utility in many data mining applications. |
| Databáze: | OpenAIRE |
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