In bioinformatics, the EzTaxon database is a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences.[1] EzTaxon is an open access database that is produced and maintained by ChunLab, Inc.
The EzTaxon database contains sequences of type strains of prokaryotic species with validly published names. Although EzTaxon is mainly used for the routine identification of prokaryotic isolates, sequences from uncultured taxa were not included. Thus in 2012, EzTaxon was extended to include uncultured prokaryotes and the name of the database was changed to EzTaxon-e.[2]
Naming conventionedit
Taxa names included in EzTaxon-e represent groups of uncultured sequences found in public domain databases. The names included in EzTaxon-e have no standing in formal nomenclature but they were created to help in the comparison of microbial communities and diversity in nature.
New names found in EzTaxon-e are formed by adding special suffixes to Genbank sequence accession numbers of sequences (e.g. AB177171_s -> species of which the sequence entry AB177171 serves type; AB177171_g -> genus; AB177171_f -> family; AB177171_o -> order; AB177171_c -> class; AB177171_p -> phylum).
Well-known names have been preserved for historical reasons. SAR11, the famous marine inhabitant, is labeled as SAR11(order), and further divided into 4 families (SAR11-1_f to SAR11-4_f).
Based on 16S rRNA sequence phylogeny, some obviously misclassified species have been renamed using special suffixes. For example, Bacteroides pectinophilus is not an authentic member of the genus Bacteroides. However, it may represent a novel genus in the family Lachnospiraceae. Therefore, in the EzTaxon-e database, Bacteroides pectinophilus is placed under a tentatively named new genus Bacteroides_g1.
Sequences and tentative taxa that start with "4P" are products of the Roche 454 GS FLX Titanium system.
Referencesedit
^Chun, Jongsik; Lee, Jae-Hak; Jung, Yoonyoung; Kim, Myungjin; Kim, Seil; Kwon Kim, Byung; Lim, Young-Woon (2007). "EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences". International Journal of Systematic and Evolutionary Microbiology. 57 (10): 2259–2261. doi:10.1099/ijs.0.64915-0. PMID 17911292.
^Kim, OS; Cho, YJ; Lee, K; Yoon, SH; Kim, M; Na, H; Park, SC; Jeon, YS; Lee, JH; Yi, H; Won, S; Chun, J (2012). "Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species". Int J Syst Evol Microbiol. 62 (3): 716–21. doi:10.1099/ijs.0.038075-0. PMID 22140171.
January 01, 1970
eztaxon, database, bioinformatics, eztaxon, database, based, tool, identification, prokaryotes, based, ribosomal, gene, sequences, eztaxon, open, access, database, that, produced, maintained, chunlab, eztaxon, database, contains, sequences, type, strains, prok. In bioinformatics the EzTaxon database is a web based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences 1 EzTaxon is an open access database that is produced and maintained by ChunLab Inc The EzTaxon database contains sequences of type strains of prokaryotic species with validly published names Although EzTaxon is mainly used for the routine identification of prokaryotic isolates sequences from uncultured taxa were not included Thus in 2012 EzTaxon was extended to include uncultured prokaryotes and the name of the database was changed to EzTaxon e 2 Naming convention editTaxa names included in EzTaxon e represent groups of uncultured sequences found in public domain databases The names included in EzTaxon e have no standing in formal nomenclature but they were created to help in the comparison of microbial communities and diversity in nature New names found in EzTaxon e are formed by adding special suffixes to Genbank sequence accession numbers of sequences e g AB177171 s gt species of which the sequence entry AB177171 serves type AB177171 g gt genus AB177171 f gt family AB177171 o gt order AB177171 c gt class AB177171 p gt phylum Well known names have been preserved for historical reasons SAR11 the famous marine inhabitant is labeled as SAR11 order and further divided into 4 families SAR11 1 f to SAR11 4 f Based on 16S rRNA sequence phylogeny some obviously misclassified species have been renamed using special suffixes For example Bacteroides pectinophilus is not an authentic member of the genus Bacteroides However it may represent a novel genus in the family Lachnospiraceae Therefore in the EzTaxon e database Bacteroides pectinophilus is placed under a tentatively named new genus Bacteroides g1 Sequences and tentative taxa that start with 4P are products of the Roche 454 GS FLX Titanium system References edit Chun Jongsik Lee Jae Hak Jung Yoonyoung Kim Myungjin Kim Seil Kwon Kim Byung Lim Young Woon 2007 EzTaxon a web based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences International Journal of Systematic and Evolutionary Microbiology 57 10 2259 2261 doi 10 1099 ijs 0 64915 0 PMID 17911292 Kim OS Cho YJ Lee K Yoon SH Kim M Na H Park SC Jeon YS Lee JH Yi H Won S Chun J 2012 Introducing EzTaxon e a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species Int J Syst Evol Microbiol 62 3 716 21 doi 10 1099 ijs 0 038075 0 PMID 22140171 Retrieved from https en wikipedia org w index php title EzTaxon Database amp oldid 994742603, wikipedia, wiki, book, books, library,
