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What is BLISS?

The BLISS website (Breaker Lab Intergenic Sequence Server) contains BLAST comparisons of intergenic regions (IGRs) from (mostly) microbial genomes. It displays alignments of similar sequences to a chosen IGR with accompanying information about nearby genes, sequence statistics, phylogenetic distributions, intrinsic terminators, and known RNA elements. We have used it mainly to search for regulatory RNA motifs that have not been previously identified. These motifs are candidates for novel riboswitches. For more information on our research, please visit the Breaker Lab Website.

Resources

Current BLISS Site

Collaborative annotation of intergenic region sequence comparisons between 116 microbial genomes.

Reference: Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick N, Breaker RR. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria Genome Biol. 6: R70 (2005). [ Pubmed ]

Archived BLISS Site

Static release of BLISS for Bacillus subtilis intergenic regions against 93 other microbial genomes.

Reference: Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR. New RNA Motifs Suggest an Expanded Scope for Riboswitches in Bacterial Genetic Control. Proc. Natl. Acad. Sci USA 101: 6421-6426 (2004). [ Pubmed ] [ Supplementary Information ]

Supplementary Data

Reference: Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA 11:774-84 (2005). [ Pubmed ] [ Supplementary Information ]

Links

• Rfam Database - contains updated sequence alignments of most of the RNA elements and riboswitches described in our papers.

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