Por favor, use este identificador para citar o enlazar a este item:
http://hdl.handle.net/10261/103580
COMPARTIR / EXPORTAR:
SHARE CORE BASE | |
Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL | DATACITE | |
Campo DC | Valor | Lengua/Idioma |
---|---|---|
dc.contributor.author | Yarza, Pablo | - |
dc.contributor.author | Richter, Michael | - |
dc.contributor.author | Pepiles, Jörg | - |
dc.contributor.author | Euzéby, Jean | - |
dc.contributor.author | Amann, Rudolf | - |
dc.contributor.author | Schleifer, Karl-Heinz | - |
dc.contributor.author | Ludwig, Wolfgang | - |
dc.contributor.author | Glöckner, Frank Oliver | - |
dc.contributor.author | Rosselló-Mora, Ramón | - |
dc.date.accessioned | 2014-10-20T12:41:08Z | - |
dc.date.available | 2014-10-20T12:41:08Z | - |
dc.date.issued | 2008-09 | - |
dc.identifier | doi: 10.1016/j.syapm.2008.07.001 | - |
dc.identifier | issn: 0723-2020 | - |
dc.identifier.citation | Systematic and Applied Microbiology 31(4): 241-250 (2008) | - |
dc.identifier.uri | http://hdl.handle.net/10261/103580 | - |
dc.description.abstract | The signing authors together with the journal Systematic and Applied Microbiology (SAM) have started an ambitious project that has been conceived to provide a useful tool especially for the scientific microbial taxonomist community. The aim of what we have called >The All-Species Living Tree> is to reconstruct a single 16S rRNA tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria. This tree is to be regularly updated by adding the species with validly published names that appear monthly in the Validation and Notification lists of the International Journal of Systematic and Evolutionary Microbiology. For this purpose, the SAM executive editors, together with the responsible teams of the ARB, SILVA, and LPSN projects (www.arb-home.de, www.arb-silva.de, and www.bacterio.cict.fr, respectively), have prepared a 16S rRNA database containing over 6700 sequences, each of which represents a single type strain of a classified species up to 31 December 2007. The selection of sequences had to be undertaken manually due to a high error rate in the names and information fields provided for the publicly deposited entries. In addition, from among the often occurring multiple entries for a single type strain, the best-quality sequence was selected for the project. The living tree database that SAM now provides contains corrected entries and the best-quality sequences with a manually checked alignment. The tree reconstruction has been performed by using the maximum likelihood algorithm RAxML. The tree provided in the first release is a result of the calculation of a single dataset containing 9975 single entries, 6728 corresponding to type strain gene sequences, as well as 3247 additional high-fquality sequences to give robustness to the reconstruction. Trees are dynamic structures that change on the basis of the quality and availability of the data used for their calculation. Therefore, the addition of new type strain sequences in further subsequent releases may help to resolve certain branching orders that appear ambiguous in this first release. On the web sites: www.elsevier.de/syapm and www.arb-silva.de/living-tree, the All-Species Living Tree team will release a regularly updated database compatible with the ARB software environment containing the whole 16S rRNA dataset used to reconstruct >The All-Species Living Tree>. As a result, the latest reconstructed phylogeny will be provided. In addition to the ARB file, a readable multi-FASTA universal sequence editor file with the complete alignment will be provided for those not using ARB. There is also a complete set of supplementary tables and figures illustrating the selection procedure and its outcome. It is expected that the All-Species Living Tree will help to improve future classification efforts by simplifying the selection of the correct type strain sequences. For queries, information updates, remarks on the dataset or tree reconstructions shown, a contact email address has been created (living-tree@arb-silva.de). This provides an entry point for anyone from the scientific community to provide additional input for the construction and improvement of the first tree compiling all sequenced type strains of all prokaryotic species for which names had been validly published. © 2008 Elsevier GmbH. All rights reserved. | - |
dc.description.sponsorship | The authors want to acknowledge the Max Planck Society and the Project Consolider (CE-CSD2007-0005) of the CICYT for funding support | - |
dc.publisher | Elsevier | - |
dc.rights | closedAccess | - |
dc.subject | Taxa boundaries | - |
dc.subject | Classification | - |
dc.subject | Taxonomy | - |
dc.subject | ARB | - |
dc.subject | Living tree | - |
dc.subject | Species | - |
dc.subject | 16S rRNA | - |
dc.subject | SSU | - |
dc.subject | Phylogeny | - |
dc.title | The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains | - |
dc.type | artículo | - |
dc.identifier.doi | 10.1016/j.syapm.2008.07.001 | - |
dc.relation.publisherversion | http://dx.doi.org/10.1016/j.syapm.2008.07.001 | - |
dc.date.updated | 2014-10-20T12:41:09Z | - |
dc.description.version | Peer Reviewed | - |
dc.language.rfc3066 | eng | - |
dc.type.coar | http://purl.org/coar/resource_type/c_6501 | es_ES |
item.fulltext | No Fulltext | - |
item.openairecristype | http://purl.org/coar/resource_type/c_18cf | - |
item.cerifentitytype | Publications | - |
item.grantfulltext | none | - |
item.openairetype | artículo | - |
Aparece en las colecciones: | (IMEDEA) Artículos |
Ficheros en este ítem:
Fichero | Descripción | Tamaño | Formato | |
---|---|---|---|---|
accesoRestringido.pdf | 15,38 kB | Adobe PDF | Visualizar/Abrir |
CORE Recommender
SCOPUSTM
Citations
778
checked on 18-abr-2024
WEB OF SCIENCETM
Citations
720
checked on 25-feb-2024
Page view(s)
804
checked on 23-abr-2024
Download(s)
299
checked on 23-abr-2024
Google ScholarTM
Check
Altmetric
Altmetric
NOTA: Los ítems de Digital.CSIC están protegidos por copyright, con todos los derechos reservados, a menos que se indique lo contrario.