De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.

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...

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Autores principales:	Christopher A Gulvik, T Chad Effler, Steven W Wilhelm, Alison Buchan
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/01dc16b1e71749d8b8fcb503bbc87470
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spelling	oai:doaj.org-article:01dc16b1e71749d8b8fcb503bbc874702021-11-18T08:07:34ZDe-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.1932-620310.1371/journal.pone.0050362https://doaj.org/article/01dc16b1e71749d8b8fcb503bbc874702012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23189198/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Development 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.Christopher A GulvikT Chad EfflerSteven W WilhelmAlison BuchanPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 11, p e50362 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Christopher A Gulvik T Chad Effler Steven W Wilhelm Alison Buchan De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.
description	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.
format	article
author	Christopher A Gulvik T Chad Effler Steven W Wilhelm Alison Buchan
author_facet	Christopher A Gulvik T Chad Effler Steven W Wilhelm Alison Buchan
author_sort	Christopher A Gulvik
title	De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.
title_short	De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.
title_full	De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.
title_fullStr	De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.
title_full_unstemmed	De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.
title_sort	de-metast-blast: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/01dc16b1e71749d8b8fcb503bbc87470
work_keys_str_mv	AT christopheragulvik demetastblastatoolforthevalidationofdegenerateprimersetsanddataminingofpubliclyavailablemetagenomes AT tchadeffler demetastblastatoolforthevalidationofdegenerateprimersetsanddataminingofpubliclyavailablemetagenomes AT stevenwwilhelm demetastblastatoolforthevalidationofdegenerateprimersetsanddataminingofpubliclyavailablemetagenomes AT alisonbuchan demetastblastatoolforthevalidationofdegenerateprimersetsanddataminingofpubliclyavailablemetagenomes
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De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.

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