Database for bacterial group II introns

• Published in: Nucleic acids research 2012-01, Vol.40 (D1), p.D187-D190
• Main Authors: Candales, Manuel A., Duong, Adrian, Hood, Keyar S., Li, Tony, Neufeld, Ryan A. E., Sun, Runda, McNeil, Bonnie A., Wu, Li, Jarding, Ashley M., Zimmerly, Steven
• Format: Article
• Language: English
• Subjects: Bacteria; Bacteria - genetics; Base Sequence; Data processing; Databases, Nucleic Acid; DNA, Bacterial - chemistry; genomics; Introns; Molecular Sequence Data; Nucleotide sequence; Protein structure; RNA; RNA, Bacterial - chemistry; Secondary structure; Software
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkr1043

The Database for Bacterial Group II Introns (http://webapps2.ucalgary.ca/~groupii/index.html#) provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. The website is divided into three sections. The first section provides general information on group II intron properties, structures and classification. The second and main section lists information for individual introns, including insertion sites, DNA sequences, intron-encoded protein sequences and RNA secondary structure models. The final section provides tools for identification and analysis of intron sequences. These include a step-by-step guide to identify introns in genomic sequences, a local BLAST tool to identify closest intron relatives to a query sequence, and a boundary-finding tool that predicts 5′ and 3′ intron-exon junctions in an input DNA sequence. Finally, selected intron data can be downloaded in FASTA format. It is hoped that this database will be a useful resource not only to group II intron and RNA researchers, but also to microbiologists who encounter these unexpected introns in genomic sequences.