TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels
The high level of conservation of 16S ribosomal RNA gene (16S rRNA) in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II) and the Greengenes Project offer access to sets o...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2010-07-01
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| Series: | Diversity |
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| Online Access: | http://www.mdpi.com/1424-2818/2/7/1015/ |
| _version_ | 1811303843898589184 |
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| author | Eric W. Triplett David B. Crabb Austin G. Davis-Richardson Adriana Giongo |
| author_facet | Eric W. Triplett David B. Crabb Austin G. Davis-Richardson Adriana Giongo |
| author_sort | Eric W. Triplett |
| collection | DOAJ |
| description | The high level of conservation of 16S ribosomal RNA gene (16S rRNA) in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II) and the Greengenes Project offer access to sets of ribosomal RNA sequence databases useful in identification of microbes in a culture-independent analysis of microbial communities. However, these databases do not contain all of the taxonomic levels attached to the published names of the bacterial and archaeal sequences. TaxCollector is a set of scripts developed in Python language that attaches taxonomic information to all 16S rRNA sequences in the RDP-II and Greengenes databases. These modified databases are referred to as TaxCollector databases, which when used in conjunction with BLAST allow for rapid classification of sequences from any environmental or clinical source at six different taxonomic levels, from domain to species. The TaxCollector database prepared from the RDP-II database is an important component of a new 16S rRNA pipeline called PANGEA. The usefulness of TaxCollector databases is demonstrated with two very different datasets obtained using samples from a clinical setting and an agricultural soil. The six TaxCollector scripts are freely available on http://taxcollector.sourceforge.net and on http://www.microgator.org. |
| first_indexed | 2024-04-13T07:55:22Z |
| format | Article |
| id | doaj.art-0738962376024b1794c693e94d5be0b2 |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-04-13T07:55:22Z |
| publishDate | 2010-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diversity |
| spelling | doaj.art-0738962376024b1794c693e94d5be0b22022-12-22T02:55:25ZengMDPI AGDiversity1424-28182010-07-01271015102510.3390/d2071015TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic LevelsEric W. TriplettDavid B. CrabbAustin G. Davis-RichardsonAdriana GiongoThe high level of conservation of 16S ribosomal RNA gene (16S rRNA) in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II) and the Greengenes Project offer access to sets of ribosomal RNA sequence databases useful in identification of microbes in a culture-independent analysis of microbial communities. However, these databases do not contain all of the taxonomic levels attached to the published names of the bacterial and archaeal sequences. TaxCollector is a set of scripts developed in Python language that attaches taxonomic information to all 16S rRNA sequences in the RDP-II and Greengenes databases. These modified databases are referred to as TaxCollector databases, which when used in conjunction with BLAST allow for rapid classification of sequences from any environmental or clinical source at six different taxonomic levels, from domain to species. The TaxCollector database prepared from the RDP-II database is an important component of a new 16S rRNA pipeline called PANGEA. The usefulness of TaxCollector databases is demonstrated with two very different datasets obtained using samples from a clinical setting and an agricultural soil. The six TaxCollector scripts are freely available on http://taxcollector.sourceforge.net and on http://www.microgator.org.http://www.mdpi.com/1424-2818/2/7/1015/16S rRNA genemicrobial diversitytaxonomy |
| spellingShingle | Eric W. Triplett David B. Crabb Austin G. Davis-Richardson Adriana Giongo TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels Diversity 16S rRNA gene microbial diversity taxonomy |
| title | TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels |
| title_full | TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels |
| title_fullStr | TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels |
| title_full_unstemmed | TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels |
| title_short | TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels |
| title_sort | taxcollector modifying current 16s rrna databases for the rapid classification at six taxonomic levels |
| topic | 16S rRNA gene microbial diversity taxonomy |
| url | http://www.mdpi.com/1424-2818/2/7/1015/ |
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