Reference: Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick N, Breaker RR. submitted. [ Supplementary Information ]

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 ]

The BLISS website is mainly intended to be an internal tool for the Breaker Lab. It is not meant to be an up-to-date database of microbial genetic regulation. It may contain incorrect annotations and out of date information. It is not meant to be a stable web resource and is subject to change without notice as we adapt it to our use. We provide access to the general scientific public as extra background for our work and with the hope that it may prove useful. We can answer limited questions about its use by e-mail.

The BLISS website is mainly intended to be an internal tool for the Breaker Lab. It is not meant to be an up-to-date database of microbial genetic regulation. It may contain incorrect annotations and out-of-date information. It is not meant to be a stable web resource and is subject to change without notice as we adapt it to our use. We provide access to the general scientific public as extra background for our work and with the hope that it may prove useful. We can answer limited questions about its use by e-mail.

Reference: Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick N, Breaker RR. submitted. [ Supplementary Information? ]

Reference: Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick N, Breaker RR. submitted. [ 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 ]

What is BLISS?

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

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

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. submitted. [ Supplementary Information? ]

Reference: Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick N, Breaker RR. submitted. [ Supplementary Information? ]

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

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 ]

Links

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

Disclaimer

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 ]

Resources

• Archived BLISS Site - Static release of BLISS for Bacillus subtilis

What is BLISS?

Supplementary Information

• 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 ]

Current BLISS Site

Reference: Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick N, Breaker RR. submitted. [ Supplementary Information? ]

Archived BLISS Site

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 ]

• Current BLISS Site - Interactive annotation of regulons in bacterial intergenic regions. (Password Protected)

• "New RNA Motifs Suggest an Expanded Scope for Riboswitches in Bacterial Genetic Control" Barrick et al. and Breaker. (submitted) [ Supplementary Information ]

• 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 ]

• "New RNA Motifs Suggest an Expanded Scope for Riboswitches in Bacterial Genetic Control" Barrick et al. and Breaker. (submitted) [Supplementary Information]

• "New RNA Motifs Suggest an Expanded Scope for Riboswitches in Bacterial Genetic Control" Barrick et al. and Breaker. (submitted) [ Supplementary Information ]

• Current BLISS Site - Interactive annotation of regulons in bacterial intergenic regions.

• Current BLISS Site - Interactive annotation of regulons in bacterial intergenic regions. (Password Protected)

• Bacillus subtilis riboswitch candidates

• "New RNA Motifs Suggest an Expanded Scope for Riboswitches in Bacterial Genetic Control" Barrick et al. and Breaker. (submitted) [Supplementary Information]

About this site.?

• Current BLISS Site - Interactive annotation of regulons in bacterial intergenic regions.

• Current BLISS Site - Interactive annotation of regulons in bacterial intergenic regions.

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• Current BLISS Site - Interactive annotation of regulons in bacterial intergenic regions. Password Protected
• Archived BLISS Site - Static release of BLISS for Bacillus subtilis
• Terminator List - Genes correlated with 5' UTR terminators across all genomes.

• Current BLISS Site - Interactive annotation of regulons in bacterial intergenic regions.
• Archived BLISS Site - Static release of BLISS for Bacillus subtilis

Resources

• Current BLISS Site - Interactive annotation of regulons in bacterial intergenic regions. Password Protected
• Archived BLISS Site - Static release of BLISS for Bacillus subtilis
• Terminator List - Genes correlated with 5' UTR terminators across all genomes.

Supplementary Information

• Bacillus subtilis riboswitch candidates

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Welcome to TWiki, a web-based collaboration tool, document management tool and knowledge base tool.

WelcomeGuest: TWiki is a web-based collaboration tool, web authoring tool, document management tool and knowledge base tool. You can edit any TWiki page.

The TWiki home is at
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The TWiki home is at
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• If you are not familiar with the TWiki collaboration tool, please visit WelcomeGuest in TWiki.TWiki first.

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• How to edit text:
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Welcome to TWiki, a web based collaboration tool, document management tool and knowledge base tool.

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Welcome to the home of TWiki.Main. This is a web based collaboration area to get to know the TWiki tool.

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Good starting points at the TWiki.Main web are listed below:

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Welcome to the home of TWiki.Main. This is a web based collaboration area to get to know the TWiki tool.

Welcome to the home of TWiki.Main. This is a web based collaboration area to get to know the TWiki tool.

The TWiki home is at
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The TWiki home is at
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Good starting points at the TWiki.Main web are:

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Welcome to the home of TWiki.Main. This is a web based collaboration area to get to know the TWiki tool.

Welcome to the home of TWiki.Main. This is a web based collaboration area to get to know the TWiki tool.

Good starting points at the TWiki.Main web are:

• WelcomeGuest?: Look here first to get you rolling on TWiki.
• TWikiWeb?: Explains what a TWiki web is.
• TWikiUsers: List of visitors to this TWiki web.

Good starting points at the TWiki.Main web are:

• WelcomeGuest?: Look here first to get you rolling on TWiki.
• TWikiWeb?: Explains what a TWiki web is.
• TWikiUsers: List of visitors to this TWiki web.

• TestArea?: The place to get your virtual TWiki hands dirty!

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The TWiki home is at
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The TWiki home is at http://www.mindspring.net/~peterthoeny/twiki/index.html

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The TWiki home is at http://www.mindspring.net/~peterthoeny/twiki/index.html

Good starting points at the TWiki.Main web are:

• WelcomeGuest?: Look here first to get you rolling on TWiki.
• TWikiWeb?: Explains what a TWiki web is.
• TWikiUsers: List of visitors to this TWiki web.

• GoodStyle?: Things to consider when changing text.
• TextFormattingRules?: Easy to learn rules when editing text.
• TextFormattingFAQ?: Answers to frequently asked questions about text formatting.
• TestArea?: The place to get your virtual TWiki hands dirty!

• Topic index: List up all TWiki.Main topics in alphabetical order.
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