The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy
| Type | : | ACL |
|---|---|---|
| Nature | : | Production scientifique |
| Au bénéfice du Laboratoire | : | Oui |
| Statut de publication | : | Publié |
| Année de publication | : | 2013 |
| Auteurs (32) | : | GUILLOU Laure BACHAR Dipankar AUDIC Stéphane BASS David BERNEY Cédric 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 MAHÉ Frédéric MASSANA Ramon MONTRESOR Marina MORARD Raphael NOT Fabrice PAWLOWSKI Lionel PROBERT Ian SAUVADET Anne-laure SIANO Raffaele STOECK Thorsten VAULOT Daniel ZIMMERMANN Pascal CHRISTEN Richard |
| Revue scientifique | : | Nucleic Acids Research |
| Volume | : | 41 |
| Fascicule | : | 0 |
| Pages | : | |
| DOI | : | 10.1093/nar/gks1160 |
| URL | : | <go to isi>://wos:000312893300085 |
| Abstract | : | 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://ssu-rrna.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 high-troughput 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. |
| Mots-clés | : | - |
| Commentaire | : | Times Cited: 18 Sauvadet, Anne-Laure/D-2349-2010; del Campo, Javier/B-5233-2008; Dolan, John/A-4513-2009 del Campo, Javier/0000-0002-5292-1421; 18 |
| Tags | : | - |
| Fichier attaché | : | - |
| Citation | : |
Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, De Vargas C, Decelle J, Del Campo J, Dolan JR, Dunthorn M, Edvardsen B, Holzmann M, Kooistra WHCF, Lara E, Le bescot N, Logares R, Mahé F, Massana R, Montresor M, Morard R, Not F, Pawlowski L, Probert I, Sauvadet A-L, Siano R, Stoeck T, Vaulot D, Zimmermann P, Christen R (2013) The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucl Acids Res 41 | doi: 10.1093/nar/gks1160
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