An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).

Comparative analysis of small-subunit ribosomal RNA (ss-rRNA) gene sequences forms the basis for much of what we know about the phylogenetic diversity of both cultured and uncultured microorganisms. As sequencing costs continue to decline and throughput increases, sequences of ss-rRNA genes are bein...

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Autores principales:	Dongying Wu, Amber Hartman, Naomi Ward, Jonathan A Eisen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/de1cb5df00944db6856ef291399201d4
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spelling	oai:doaj.org-article:de1cb5df00944db6856ef291399201d42021-11-25T06:11:47ZAn automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).1932-620310.1371/journal.pone.0002566https://doaj.org/article/de1cb5df00944db6856ef291399201d42008-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18596968/?tool=EBIhttps://doaj.org/toc/1932-6203Comparative analysis of small-subunit ribosomal RNA (ss-rRNA) gene sequences forms the basis for much of what we know about the phylogenetic diversity of both cultured and uncultured microorganisms. As sequencing costs continue to decline and throughput increases, sequences of ss-rRNA genes are being obtained at an ever-increasing rate. This increasing flow of data has opened many new windows into microbial diversity and evolution, and at the same time has created significant methodological challenges. Those processes which commonly require time-consuming human intervention, such as the preparation of multiple sequence alignments, simply cannot keep up with the flood of incoming data. Fully automated methods of analysis are needed. Notably, existing automated methods avoid one or more steps that, though computationally costly or difficult, we consider to be important. In particular, we regard both the building of multiple sequence alignments and the performance of high quality phylogenetic analysis to be necessary. We describe here our fully-automated ss-rRNA taxonomy and alignment pipeline (STAP). It generates both high-quality multiple sequence alignments and phylogenetic trees, and thus can be used for multiple purposes including phylogenetically-based taxonomic assignments and analysis of species diversity in environmental samples. The pipeline combines publicly-available packages (PHYML, BLASTN and CLUSTALW) with our automatic alignment, masking, and tree-parsing programs. Most importantly, this automated process yields results comparable to those achievable by manual analysis, yet offers speed and capacity that are unattainable by manual efforts.Dongying WuAmber HartmanNaomi WardJonathan A EisenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 3, Iss 7, p e2566 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Dongying Wu Amber Hartman Naomi Ward Jonathan A Eisen An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).
description	Comparative analysis of small-subunit ribosomal RNA (ss-rRNA) gene sequences forms the basis for much of what we know about the phylogenetic diversity of both cultured and uncultured microorganisms. As sequencing costs continue to decline and throughput increases, sequences of ss-rRNA genes are being obtained at an ever-increasing rate. This increasing flow of data has opened many new windows into microbial diversity and evolution, and at the same time has created significant methodological challenges. Those processes which commonly require time-consuming human intervention, such as the preparation of multiple sequence alignments, simply cannot keep up with the flood of incoming data. Fully automated methods of analysis are needed. Notably, existing automated methods avoid one or more steps that, though computationally costly or difficult, we consider to be important. In particular, we regard both the building of multiple sequence alignments and the performance of high quality phylogenetic analysis to be necessary. We describe here our fully-automated ss-rRNA taxonomy and alignment pipeline (STAP). It generates both high-quality multiple sequence alignments and phylogenetic trees, and thus can be used for multiple purposes including phylogenetically-based taxonomic assignments and analysis of species diversity in environmental samples. The pipeline combines publicly-available packages (PHYML, BLASTN and CLUSTALW) with our automatic alignment, masking, and tree-parsing programs. Most importantly, this automated process yields results comparable to those achievable by manual analysis, yet offers speed and capacity that are unattainable by manual efforts.
format	article
author	Dongying Wu Amber Hartman Naomi Ward Jonathan A Eisen
author_facet	Dongying Wu Amber Hartman Naomi Ward Jonathan A Eisen
author_sort	Dongying Wu
title	An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).
title_short	An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).
title_full	An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).
title_fullStr	An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).
title_full_unstemmed	An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).
title_sort	automated phylogenetic tree-based small subunit rrna taxonomy and alignment pipeline (stap).
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/de1cb5df00944db6856ef291399201d4
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An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).

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