Journal: Journal of Clinical Microbiology
Article Title: Evaluation of the Integrated Database Network System (IDNS) SmartGene Software for Analysis of 16S rRNA Gene Sequences for Identification of Nocardia Species ▿
doi: 10.1128/JCM.00681-10
Figure Lengend Snippet: Discordant results from searches of type strain sequences with the centroid database c
Article Snippet: The selection of short centroids is related to the small number of available sequences in the public databases for some species; this error might be corrected by the selection of only full-length (or nearly full-length) sequences as centroid sequences, if such sequences exist. table ft1 table-wrap mode="anchored" t5 TABLE 2. caption a7 Species Strain No. of: Results Centroid database Best match(es) in eubacteria database Clinical isolates tested Isolates in centroid group Best match(es) % similarity of match Source(s) of discrepant results Error type b N. aobensis DSM 44805 0 6 N. africana 99.2 Short centroid 1 N. aobensis N. cyriacigeorgica DSM 44484 5 52 N. abscessus 98.8 Short centroid 1 N. cyriacigeorgica N. shimofusensis a DSM 44733 0 4 N. higoensis 99.2 Short centroid 1 N. shimofusensis N. transvalensis ATCC 6865 0 28 N. blacklockiae 98.8 Incorrect centroid 2A N. transvalensis N. wallacei 98.6 N. transvalensis 98.6 N. wallacei a ATCC 49873 4 2 N. wallacei 100 Incorrect centroid for N. transvalensis 2B N. wallacei N. transvalensis 99.9 N. beijingensis DSM 44636 4 24 N. beijingensis 100 Probable incorrect identification of S . gardneri in public database 2B N. beijingensis S. gardneri 99.9 S. gardneri N. ninae a DSM 44978 0 1 N. ninae 99.7 Few sequences in public database; errors in those sequences 2C N. ninae N. pneumoniae a DSM 44730 1 2 N. pneumoniae 99.4 Few sequences in public database; errors in those sequences 2C N. pneumoniae N. otitidiscaviarum ATCC 14629 2 24 N. otitidiscaviarum 99.7 Heterogeneous sequences in species group 3 N. otitidiscaviarum Open in a separate window a Centroid is the sequence of the type strain of the species. b Error type 1, short sequence selected as centroid; error type 2, inaccurate or insufficient entries in the public database (error types 2A and 2B, inaccurate information in the public database; error type 2C, possible sequence errors in type strains); error type 3, heterogeneous sequences of members of a species. c Clinical isolates have results identical to those of the type strains.
Techniques:
DSMZ is a verified supplier 
