Table 2.
Comparison of 16SpathDB and other commonly used software for bacterial identification using 16S rRNA gene sequencing
| Software | Yr of first description | Company/organization | Website | Partial/full 16S rRNA gene sequence included | Database size | Source of sequences | Cost | Quality control | Updates |
|---|---|---|---|---|---|---|---|---|---|
| Ribosomal Database Project (RDP) | 1992 | Michigan State University, East Lansing, MI | http://rdp.cme.msu.edu/ | Partial and full | 1,418,497 (release 10.22) | GenBank | No | Partial | Periodically |
| MicroSeq Microbial Identification Systema | 1998 | Applied Biosystems, Foster City, California | http://www.microseq.com | Partial and fulla | 1,834 and 1,261 in the two databases, respectivelya | Sequence of 16S rRNA gene of one strain from each species | Yes | All type strains from culture collections | Periodically |
| Ribosomal Differentiation of Medical Microorganisms (RIDOM) | 1999 | Ridom GmbH, Würzburg, Germany | http://rdna2.ridom.de/ | Partial | 236b | Sequences of 16S rRNA genes of medically relevant bacteria, mainly belonging to the Neisseriaceae, Moraxellaceae, and genus Mycobacterium | No | All strains from culture collections | Periodically |
| SmartGene IDNS software | 2006 | SmartGene GmbH, Switzerland | http://www.smartgene.com/mod_bacteria.html | Partial and full | 243,000 | GenBank | Yes | Partial | Daily |
| 16SpathDB | 2010 | Department of Microbiology, University of Hong Kong, Hong Kong | http://147.8.74.24/16SpathDB | Partial and full | 1,010 | GenBank | No | All sequences manually selected from GenBank | Periodically |
a
Contains two databases, MicroSeq ID 16S rDNA 500 Library v2.2, which contains sequences from the 5′-end 527 bp of 16S rRNA genes, and MicroSeq ID 16S rDNA Full Gene Library v2.0, which contains full 16S rRNA gene sequences.
b
Number from from http://rdna2.ridom.de/ridom2/servlet/link?page = list (8 Nov 2010).