| Registro completo |
| Provedor de dados: |
ArchiMer
|
| País: |
France
|
| Título: |
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy
|
| Autores: |
Guillou, Laure
Bachar, Dipankar
Audic, S
Bass, David
Berney, Cedric
Bittner, Lucie
Boutte, Christophe
Burgaud, Gaetan
De Vargas, Colomban
Decelle, Johan
Del Campo, Javier
Dolan, John R.
Dunthorn, Micah
Edvardsen, Bente
Holzmann, Maria
Kooistra, Wiebe H. C. F.
Lara, Enrique
Le Bescot, Noan
Logares, Ramiro
Mahe, F
Massana, Ramon
Montresor, Marina
Morard, Raphael
Not, Fabrice
Pawlowski, Jan
Probert, Ian
Sauvadet, Anne-laure
Siano, Raffaele
Stoeck, Thorsten
Vaulot, Daniel
Zimmermann, Pascal
Christen, Richard
|
| Data: |
2013-01
|
| Ano: |
2013
|
| Resumo: |
The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssurrna. org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of hightroughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.
|
| Tipo: |
Text
|
| Idioma: |
Inglês
|
| Identificador: |
http://archimer.ifremer.fr/doc/00114/22492/20174.pdf
DOI:10.1093/nar/gks1160
|
| Editor: |
Oxford Univ Press
|
| Relação: |
http://archimer.ifremer.fr/doc/00114/22492/
|
| Formato: |
application/pdf
|
| Fonte: |
Nucleic Acids Research (0305-1048) (Oxford Univ Press), 2013-01 , Vol. 41 , N. D1 , P. D597-D604
|
| Direitos: |
The Author(s) 2012. Published by Oxford University Press.
|
|
