16SDB7: a comprehensive database of 16S sequences

16SDB7 is a database of RNA 16S sequences that has been developed by Era7 Bioinformatics. The RNA 16S sequences are automatically curated through a procedure that extracts the information from RNAcentral. Our database is open and is included as a featured case in the section Featured use cases within the RNAcentral homepage.

16SDB7

 

16SDB7 sequences

16SDB7 is a database of sequences 16S extracted from RNAcentral [1] database, the most comprehensive compilation of non-conding RNA sequences.

Sequences from RNAcentral are included in our database if they satisfy all of the following:

  • The sequence is annotated as rRNA
  • The sequence contains no unambiguous nucleotides (only ATGC)
  • Its header description in some of the source databases contains the string 16S / 16s
  • It is present in at least one open database

The majority of the 16S sequences collected from RNAcentral following those criteria comes from the following databases:

 

Number of sequences in 16SDB7

In total, for its last release, 16SDB7 includes around 6 millions of 16S sequences from RNAcentral to be used as reference sequences.

 

References

  1. RNAcentral: a hub of information for non-coding RNA sequences. Blake A Sweeney, Anton I Petrov, Boris Burkov, Robert D Finn, Alex Bateman, Maciej Szymanski, Wojciech M Karlowski, Jan Gorodkin, Stefan E Seemann, Jamie J Cannone, Robin R Gutell, Petra Fey, Siddhartha Basu, Simon Kay, Guy Cochrane, Kostantinos Billis, David Emmert, Steven J Marygold, Rachael P Huntley, Ruth C Lovering, Adam Frankish, Patricia P Chan, Todd M Lowe, Elspeth Bruford, Ruth Seal, Jo Vandesompele, Pieter-Jan Volders, Maria Paraskevopoulou, Lina Ma, Zhang Zhang, Sam Griffiths-Jones, Janusz M Bujnicki, Pietro Boccaletto, Judith A Blake, Carol J Bult, Runsheng Chen, Yi Zhao, Valerie Wood, Kim Rutherford, Elena Rivas, James Cole, Stanley J F Laulederkind, Mary Shimoyama, Marc E Gillespie, Marija Orlic-Milacic, Ioanna Kalvari, Eric Nawrocki, Stacia R Engel, J Michael Cherry, SILVA Team, Tanya Z Berardini, Artemis Hatzigeorgiou, Dimitra Karagkouni, Kevin Howe, Paul Davis, Marcel Dinger, Shunmin He, Maki Yoshihama, Naoya Kenmochi, Peter F Stadler, and Kelly P Williams. Nucleic Acids Research 47 (D1 2019), D221–D229. DOI: 10.1093/nar/gky1034.