| Title |
De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes
|
|---|---|
| Published in |
PLOS ONE, November 2012
|
| DOI | 10.1371/journal.pone.0050362 |
| Pubmed ID | |
| Authors |
Christopher A. Gulvik, T. Chad Effler, Steven W. Wilhelm, Alison Buchan |
| 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, this search tool has potential utility in many data mining applications. |
X Demographics
The data shown below were collected from the profiles of 6 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Australia | 1 | 17% |
| Sweden | 1 | 17% |
| United States | 1 | 17% |
| Germany | 1 | 17% |
| Unknown | 2 | 33% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 3 | 50% |
| Scientists | 3 | 50% |
Mendeley readers
The data shown below were compiled from readership statistics for 92 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 2 | 2% |
| Brazil | 1 | 1% |
| Sweden | 1 | 1% |
| Chile | 1 | 1% |
| India | 1 | 1% |
| South Africa | 1 | 1% |
| Estonia | 1 | 1% |
| Luxembourg | 1 | 1% |
| Unknown | 83 | 90% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 23 | 25% |
| Student > Ph. D. Student | 22 | 24% |
| Student > Master | 11 | 12% |
| Student > Bachelor | 9 | 10% |
| Student > Doctoral Student | 6 | 7% |
| Other | 13 | 14% |
| Unknown | 8 | 9% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 49 | 53% |
| Biochemistry, Genetics and Molecular Biology | 12 | 13% |
| Environmental Science | 6 | 7% |
| Computer Science | 4 | 4% |
| Immunology and Microbiology | 2 | 2% |
| Other | 8 | 9% |
| Unknown | 11 | 12% |