Breaker Lab Bioinformatics > WebHome (book view)
	Breaker Lab | Changes | Index | Search | Go

About 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 Riboswitches and other possible regulatory RNAs. For more information on our research, please visit the Breaker Lab Website.

Disclaimer

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 It may contain incorrect annotations and out of date information.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.

• Name: AdamRoth
• Email: foo@foo.bar
• Company Name:
• Company URL:
• Location: LondonOffice?
• Country: Fiji
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Alex Bateman
• Email: foo@foo.com
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: BenjaminBoese
• Email: foo@foo.bar
• Company Name:
• Company URL: http://
• Location: TokyoOffice?
• Country: Bangladesh
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Brian Tucker
• Email: foo@foo.com
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Elizabeth Regulski
• Email: elizabeth.regulski@yale.edu
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

File Attachments

Each topic can have one or more files of any type attached to it by using the Attach screen to upload (or download) files from your local PC. Attachments are stored under revision control: uploads are automatically backed up; all previous versions of a modified file can be retrieved.

What Are Attachments Good For?

File Attachments can be used to create powerful customized groupware solutions, like file sharing and document management systems, and quick Web page authoring.

Document Management System

• You can use Attachments to store and retrieve documents (in any format, with associated graphics, and other media files); attach documents to specific TWiki topics; collaborate on documents with full revision control; distribute documents on a need-to-know basis using web and topic-level access control; create a central reference library that's easy to share with an user group spread around the world.

File Sharing

• For file sharing, FileAttachments on a series of topics can be used to quickly create a well-documented, categorized digital download center for all types of files: documents; graphics and other media; drivers and patches; applications; anything you can safely upload!

Web Authoring

• Through your Web browser, you can easily upload graphics (or sound files, or anything else you want to link to on a page) and place them on a single page, or use them across a web, or site-wide.
  • NOTE: You can also add graphics - any files - directly, typically by FTP upload. This requires FTP access, and may be more convenient if you have a large number of files to load. FTP-ed files can't be managed using browser-based Attachment controls. You can use your browser to create TWikiVariables shortcuts, like this %H% = .

Uploading Files

• Click on the Attach link at the bottom of the page. The Attach screen lets you browse for a file, add a comment, and upload it. The uploaded file will show up in the File Attachment table.
  • Any type of file can be uploaded. Some files that might pose a security risk are renamed, ex: *.php files are renamed to *.php.txt so that no one can place code that would be read in a .php file.
  • The previous upload path is retained for convenience. In case you make some changes to the local file and want to upload it, again you can copy the previous upload path into the Local file field.
  • Currently there is no file size limit other than the disk space on the server. * It's not recommended to upload files greater than a few hundred K through a browser. Large files can be extremely slow-loading, and often time out. Use FTP for large file uploads.

Downloading Files

• Click on the file in the File Attachment table.

• NOTE: There is no access control on individual attachments. If you need control over single files, create a separate topic per file and set topic-level access restrictions? for each.

Moving Attachment Files

An attachment can be moved between topics.

• Click Action on the Attachment to be moved.
• On the control screen, select the new web and/or topic.
• Click Move. The attachment and its version history are moved. The original location is stored as topic Meta Data?.

Deleting Attachments

It is not possible to delete attached files directly. You can delete a topic, and its attachments with it.

• One easy workaround is to create a Trash.TrashAttachments - then, simply move unwanted Attachments to that topic.

Linking to Attached Files

• Once a file is attached it can be referenced in the topic. Example:
  1. Attach file: Sample.txt
  2. Edit topic and enter: %ATTACHURL%/Sample.txt
  3. Preview: %ATTACHURL%/Sample.txt text appears as: http://bliss.biology.yale.edu/twiki/pub/TWiki/FileAttachment/Sample.txt, a link to the text file.

• To reference an attachment located in another topic, enter:
  • %PUBURL%/%WEB%/OtherTopic/Sample.txt (if it's within the same web)
  • %PUBURL%/Otherweb/OtherTopic/Sample.txt (if it's in a different web)

• Attached HTML files and text files can be inlined in a topic. Example:
  1. Attach file: Sample.txt
  2. Edit topic and write text: %INCLUDE{"%ATTACHURL%/Sample.txt"}%
     • Content of attached file is shown inlined.
     • Read more in IncludeTopicsAndWebPages?.

• GIF, JPG and PNG images can be attached and shown embedded in a topic. Example:
  1. Attach file: Smile.gif
  2. Edit topic and write text: %ATTACHURL%/Smile.gif
  3. Preview: text appears as , an image.

File Attachment Contents Table

Files attached to a topic are displayed in a directory table, displayed at the bottom of the page, or optionally, hidden and accessed when you click Attach.

Attachment: Action: Size: Date: Who: Comment: Sample.txt action 30 22 Jul 2000 - 19:37 PeterThoeny Just a sample Smile.gif action 94 22 Jul 2000 - 19:38 PeterThoeny Smiley face

File Attachment Controls

Clicking on an Action link takes you to a new page that looks like this:

Attachment: Action: Size: Date: Who: Comment: Attribute: Sample.txt action 30 22 Jul 2000 - 19:37 PeterThoeny Just a sample   Smile.gif action 94 22 Jul 2000 - 19:38 PeterThoeny Smiley face   Update attachment Sample.txt Version: Action: Date: Who: Comment: 1.1 view 2001.08.30.09.28.56 PeterThoeny   Previous upload: C:\DATA\Sample.txt (PeterThoeny) Local file: Comment: Link: Create a link to the attached file at the end of the topic. Hide file: Hide attachment in normal topic view. Help text ... Topic FileAttachment . { | | Move attachment | Cancel }

• The first table is a list of all attachments, including their attributes. An h means the attachment is hidden, it isn't listed when viewing a topic.

• The second table is all the versions of the attachment. Click on View to see that version. If it's the most recent version, you'll be taken to an URL that always displays the latest version, which is usually what you want.
  • To change the comment on an attachment, enter a new comment and then click Change properties. Note that the comment listed against the specific version will not change, however the comment displayed when viewing the topic does change.
  • To hide/unhide an attachment, enable the Hide file checkbox, then click Change properties.

Known Issues

• Unlike topics, attachments are not locked during editing. As a workaround, you can change the comment to indicate an attachment file is being worked on - the comment on the specific version isn't lost, it's there when you list all versions of the attachment.

• Name: Gail Emilsson
• Email: gail.emilsson@yale.edu
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Inbal Jona
• Email: inbaljona@yahoo.com
• Company Name:
• Company URL:
• Location: TokyoOffice?
• Country: Armenia
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Izabela Puskarz
• Email: iz@tokio.com
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Jeffrey Barrick
• Email: jeffrey.barrick@yale.edu
• Company Name:
• Company URL:
• Location: (Please specify office location)
• Country: USA
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE = JeffreyBarrick

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Jennifer Collins
• Email: foo@foo.com
• Company Name:
• Company URL:
• Location: TokyoOffice?
• Country: Suriname
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Jinsoo Lim
• Email: fake@fake.com
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Joe Glotz
• Email: Joe@joe.com
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Keith Corbino
• Email: keith.corbino@yale.edu
• Company Name: Yale University
• Company URL: http://www.yale.edu
• Location: SanJoseOffice?
• Country: Algeria
• Comment: Comments

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Ken Wickiser
• Email: foo@foo.com
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Kristian Link
• Email: linkk_1975@yahoo.com
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Mark Lee
• Email: foo@bar.com
• Company Name:
• Company URL:
• Location: LondonOffice?
• Country: Aruba
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: MaumitaMandal
• Email: foo@foo.com
• Company Name:
• Company URL:
• Location: SanJoseOffice?
• Country: Angola
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Ming Cheah
• Email: foo@foo.com
• Company Name:
• Company URL:
• Location: LondonOffice?
• Country: Angola
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: NarasimhanSudarsan
• Email: foo@bar.com
• Company Name:
• Company URL:
• Location: SanJoseOffice?
• Country: Albania
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Noam Rudnick
• Email: bob@bob.com
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

Nobody Group

• Set GROUP =
• Set ALLOWTOPICCHANGE = TWikiAdminGroup

Used to prevent dangerous actions e.g. renaming TWikiPreferences - put NobodyGroup as the only group allowed to rename a topic and it can't be renamed.

Related topics: TWikiUsers, TWikiGroups, TWikiAccessControl

• Name: RonaldBreaker
• Email: foo@foo.com
• Company Name:
• Company URL:
• Location: SanJoseOffice?
• Country: USA
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Ruediger Welz
• Email: fake@fake.com
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Shingo Nakamura
• Email: fake@fake.com
• Company Name:
• Company URL:
• Location: LondonOffice?
• Country: Andorra
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

• Name: Sidney Altman
• Email: foo@fake.com
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

New RNA Motifs Suggest an Expanded Scope for Riboswitches in Bacterial Genetic Control (Supplementary Methods and Website)

Jeffrey E. Barrick, Keith A. Corbino, Wade C. Winkler, Ali Nahvi, Maumita Mandal, Jennifer Collins, Mark Lee, Adam Roth, Narasimhan Sudarsan, Inbal Jona, J. Kenneth Wickiser, and Ronald R. Breaker

Contents

• BLISS Overview
• Genome Sequences
• IGR Sequence Comparisons
• Gene Function Predictions
• Terminator Predictions
• IGR Annotation
• Candidate Phylogenies
• References

Links

• Archived Bacillus subtilis BLISS site
• Complete list of organisms and abbreviations
• Complete list of COGs

BLISS Overview

The BLISS database integrates comparative genomics information to enable riboswitch discovery in Bacillus subtilis. It begins with automatically generated alignments seeded by BLAST hits between intergenic regions (IGRs) from fully sequenced bacterial genomes and incorporates uniform predictions of gene functions and intrinsic terminators. A web interface to the database allows intergenic regions to be sorted based on genome position or statistics derived from its sequence alignment. An integrated system for collaborative annotation facilitates the exhaustive manual examination of these IGRs for riboswitch candidates.

Genome Sequences

A complete list of the genomes analyzed is available. Genome sequences were downloaded in Genbank format from the NCBI bacterial reference sequence list. Genes on the same strand separated by fewer than 30 nt are usually part of the same transcriptional unit (1) and are not large enough to harbor structured RNA sequences. Therefore, we only considered IGRs with a length of at least 30 nt. Organisms were classified into broad taxonomic groups based on the information in Genbank records and the Complete Microbial Resource at TIGR. Our three-letter organism abbreviations are derived from the COG database when possible.

IGR Sequence Comparisons

We used version 2.2.5 of the BLAST package to compare Bacillus subtilis intergenic regions to intergenic region databases for every other genome. The program BLASTN was used with a word size of 7 nucleotides, a gap open penalty of 2, a gap extension penalty of 2, and a nucleotide penalty of 2 (-W 7 -G 2 -E 2 -q -2). These parameters were found to maximize the ratio of known positive comparisons (hits between two riboswitches) to known negative comparisons (hits between riboswitch intergenic regions and other IGRs) with a set of known riboswitch-containing IGRs within the B. subtilis genome (J.E.B., data not shown). BLAST results were symmetrized by taking the higher E-value for each pair of unidirectional hits between two intergenic regions. Bidirectional hits with E-values <= 0.01 were individually aligned to the B. subtilis sequence using the program ssearch34 from version 3.4 of the FASTA package (2) with a gap opening penalty of 15 (-f -15).

Gene Function Predictions

We used the COG database (September 2003) to uniformly assign gene functions to the genomic data sets (3, 4). Specifically, each annotated protein gene was filtered with the COILS 2.2 program (5) and compared to proteins in the COG database using BLASTPGP with default parameters. From these similarity results proteins were assigned to COGs by the local version of the COGnitor program. Proteins that are the results of gene fusions are often assigned to multiple COGs.

Gene descriptions and names for each COG are derived from the "whog" file of the database distribution. Gene names were assigned from identified genes in a COG with the following priority: (1) If the COG contains an E. coli gene then use this name, (2) If the COG contains a B. subtilis gene then use this name, (3) Otherwise do not assign a name (designated with a dash).

Terminator Predictions

Intrinsic terminators were predicted using a the software program TransTerm available from TIGR (6). The source code was modified to (1) ignore distinctions between head-to-tail and tail-to-tail intergenic regions when scoring terminators and (2) leave separate confidence values for overlapping terminators on opposite strands. The altered source for "smooth_confidence.perl" is available. Terminators with >98% confidence are high quality predictions.

IGR Annotation

The BLISS database links intergenic regions to the open source TWiki collaboration tool. TWiki allows webpages to be edited by any registered user and supports full version control to record a history of all page edits. BLISS generates a separate TWiki webpage for each intergenic region automatically when a user chooses to add annotation. Keywords within these pages are recognized by the web interface to prominently display information on the sortable list of IGRs. Our lab has used these pages to record known riboswitches, transcription-factor binding sites, T boxes, noncoding RNAs and other sequence features in B. subtilis IGRs that cause clusters of BLAST hits. Every remaining intergenic region alignment with at least 5 sequences has been examined for conservation indicative of a regulatory RNA motif.

The archived pages presented here have editing disabled so that a snapshot of the annotation process has been preserved. See the current BLISS pages for the ongoing annotation effort.

Candidate Phylogenies

We manually aligned the BLAST hits from the most promising candidate intergenic regions to create initial models for each putative RNA structure. Matches of these RNA motifs consisting of blocks of consensus sequences and base pairing to our curated set of complete genomes were compiled using the program SequenceSniffer (J.E.B., unpublished program). This program displays the relation of matches to nearby genes so that sequences regulating related genes are readily recognized. The published RNAMotif program allows more general searching for RNA patterns (7). Further BLAST matches to the conserved sequence families were found in other organisms with the NCBI Microbial BLAST page. We iteratively relaxed the RNA consensus model with each expanded alignment and repeated these searches until no new matches could be found.

References

1. Salgado, H., Moreno-Hagelsieb, G., Smith, T.F., and Collado-Vides, J. 2000. Operons in Escherichia coli: Genomic analyses and predictions. Proc. Natl. Acad. Sci. U. S. A. 97: 6652-6657.

2. Pearson, W.R. 2000. Flexible Sequence Similarity Searching with the FASTA3 Program Package. In Bioinformatics Methods and Protocols. (eds. S. Misener, and S.A. Krawetz), pp. 185-219. Humana Press, Totowa, NJ.

3. Tatusov, R.L., Koonin, E.V., and Lipman, D.J. 1997. A genomic perspective on protein families. Science 278: 631-637.

4. Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., Tatusova, T.A., Shankavaram, U.T., Rao, B.S., Kiryutin, B., Galperin, M.Y., Fedorova, N.D., and Koonin, E.V. 2001. The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29: 22-28.

5. Lupas, A. 1996. Prediction and analysis of coiled-coil structures. Method Enzymol 266: 513-525.

6. Ermolaeva, M.D., Khalak, H.G., White, O., Smith, H.O., and Salzberg, S.L. 2000. Prediction of transcription terminators in bacterial genomes. J. Mol. Biol. 301: 27-33.

7. Macke, T.J., Ecker, D.J., Gutell, R.R., Gautheret, D., Case, D.A., and Sampath, R. 2001. RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res. 29: 4724-4735.

6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter

Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR

Supporting Data

Supplemental_File_S1.sto
Manual alignment of 121 6S RNA sequences (Stockholm format).

Supplemental_File_S2.sto
Full computational alignment of all 6S RNA sequences (Stockholm format).

Supplemental_File_S3.tree
Tree file of 121 6S RNA sequences (Phylip format).

Notes

• I recommend viewing the HTML alignnments.
• The stems and secondary structure are labeled at the bottom of the files.
• Pseudoknots are not currently annotated (or aligned correctly) in many of the files because I have to merge them in from a separate automated alignment.
• I'm still updating some of the secondary structures to go with the x-ray crystal structures.
• AAAA to aaaa represents pseudoknotted pairs.

TWiki Administrator Group

• Set GROUP = JeffreyBarrick
• Set ALLOWTOPICCHANGE = TWikiAdminGroup

(Note: Set the members of TWiki Administrator Group in GROUP, then enable the ALLOWTOPICCHANGE variable by removing # sign)

Related topics: TWikiUsers, TWikiGroups, TWikiAccessControl

-- PeterThoeny? - 28 Oct 2000

These groups can be used to define fine grained TWikiAccessControl in TWiki:

• TWikiAdminGroup

Add your groups to this list and define new group topics similar to existing ones. Group topics must end in ...Group.

IMPORTANT NOTE: Think twice before restricting write access to a web or a topic, because an open system where everybody can contribute is the essence of the WikiCulture. Experience shows that unrestricted write access works very well because:

• There is enough peer pressure to post only appropriate content.
• Content does not get lost because topics are under revision control.
• A topic revision can be undone by a member of the TWikiAdminGroup in case needed.

Related topics: TWikiAccessControl, WebPreferences, TWikiUsers, WikiCulture.

-- PeterThoeny? - 07 Nov 2000

A guest of this TWiki web, not unlike yourself. You can leave your trace behind you, just add your name in TWikiRegistration and create your own page.

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Default state of the link check box in the attach file page:
  • Set ATTACHLINKBOX =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

The site-level preferences are located in TWiki.TWikiPreferences

• Set ALLOWTOPICCHANGE = TWikiAdminGroup
• Set ALLOWTOPICRENAME = TWikiAdminGroup

-- JeffreyBarrick - 18 Sep 2005

List of TWiki users

Please take the time and add yourself to the list. To do that fill out the form in TWikiRegistration. This will create an account for you which allows you to edit topics.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

• A - - - - -
• B - - - - -
• C - - - - -
• D - - - - -
• E - - - - -
• F - - - - -
• G - - - - -
• GailEmilsson - 19 Dec 2003
• H - - - - -
• I - - - - -
• InbalJona - 04 Sep 2003
• J - - - - -
• JeffreyBarrick - 22 Sep 2003
• JenniferCollins - 05 Sep 2003
• JoeGlotz - 04 Dec 2006
• K - - - - -
• KristianLink - 07 Sep 2004
• L - - - - -
• M - - - - -
• MarkLee - 29 Aug 2003
• MingCheah - MingCheah - 29 Aug 2003
• N - - - - -
• NicholasLee? - NicholasLee? - 28 Aug 2000
• O - - - - -
• P - - - - -
• Q - - - - -
• R - - - - -
• S - - - - -
• ShingoNakamura - 16 Sep 2003
• T - - - - -
• TWikiGuest - guest - 10 Feb 1999
• U - - - - -
• V - - - - -
• W - - - - -
• X - - - - -
• Y - - - - -
• Z - - - - -

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Note: Do not edit this topic to add a user, use TWikiRegistration instead.

• Set ALLOWTOPICCHANGE = TWikiAdminGroup

Related topics: OfficeLocations?, TWikiGroups

See TWiki.TWikiVariables

• Name: WadeWinkler
• Email: wade.winkler@yale.edu
• Company Name: Yale University
• Company URL: http://riboswitches.com
• Location: SanJoseOffice?
• Country: Albania
• Comment: sfljaslfjlsdkdfjlksd

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

Number of topics: 47

• See 100, 200, 400, 800 most recent changes
• See all changes

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.

Disclaimer

Number of topics: 47

See also the faster WebTopicList

This is a subscription service to be automatically notified by e-mail when topics change in this Main web. This is a convenient service, so you do not have to come back and check all the time if something has changed. To subscribe, please add a bullet with your WikiName in alphabetical order to this list:

• TWikiGuest - example@your.company

Format: <space><space><space>, followed by:
* Main.yourWikiName (if you want that the e-mail address in your home page is used)
* Main.yourWikiName - yourEmailAddress (if you want to specify a different e-mail address)
* Main.anyTWikiGroup (if you want to notify all members of a particular TWikiGroup)

Related topics: TWikiUsers, TWikiRegistration

TWiki.Main Web Preferences

The following settings are web preferences of the TWiki.Main web. These preferences overwrite the site-level preferences in TWikiPreferences, and can be overwritten by user preferences (your personal topic, i.e. TWikiGuest in the TWiki.Main web)

Preferences:

• List of topics of the TWiki.Main web:
  • Set WEBTOPICLIST = Breaker Lab | Changes | Index | Search | Go

• Web specific background color: (Pick a lighter one of the StandardColors)
  • Set WEBBGCOLOR = #99CCFF

• List this web in the SiteMap:
  • If yes, Set SITEMAPLIST = on, and add the "what" and "use to..." description for the site map. Make sure to list only links that include the name of the web, e.g. Main.Topic links.
  • Set SITEMAPLIST = on
  • Set SITEMAPWHAT = Welcome to TWiki... Users, Groups, Offices? - tour this expandable virtual workspace.
  • Set SITEMAPUSETO = ...get a first-hand feel for TWiki possibilities.

• Exclude web from a web="all" search: (Set to on for hidden webs)
  • Set NOSEARCHALL =

• Default template for new topics and form(s) for this web:
  • WebTopicEditTemplate?: Default template for new topics in this web. (Site-level is used if topic does not exist)
  • TWiki.WebTopicEditTemplate: Site-level default template
  • TWikiForms: How to enable form(s)
  • Set WEBFORMS =

• Users or groups who are not / are allowed to view / change / rename topics in the Main web: (See TWikiAccessControl)
  • Set DENYWEBVIEW =
  • Set ALLOWWEBVIEW =
  • Set DENYWEBCHANGE =
  • Set ALLOWWEBCHANGE = TWikiAdminGroup
  • Set DENYWEBRENAME =
  • Set ALLOWWEBRENAME = TWikiAdminGroup

• Users or groups allowed to change or rename this WebPreferences topic: (I.e. TWikiAdminGroup)
  • Set ALLOWTOPICCHANGE = TWikiAdminGroup
  • Set ALLOWTOPICRENAME = TWikiAdminGroup

• Web preferences that are not allowed to be overridden by user preferences:
  • Set FINALPREFERENCES = WEBTOPICLIST, DENYWEBVIEW, ALLOWWEBVIEW, DENYWEBCHANGE, ALLOWWEBCHANGE, DENYWEBRENAME, ALLOWWEBRENAME

Notes:

• A preference is defined as:
  6 spaces * Set NAME = value
  Example:
  • Set WEBBGCOLOR = #FFFFC0
• Preferences are used as TWikiVariables by enclosing the name in percent signs. Example:
  • When you write variable %WEBBGCOLOR% , it gets expanded to #99CCFF .
• The sequential order of the preference settings is significant. Define preferences that use other preferences first, i.e. set WEBCOPYRIGHT before WIKIWEBMASTER since %WEBCOPYRIGHT% uses the %WIKIWEBMASTER% variable.
• You can introduce new preferences variables and use them in your topics and templates. There is no need to change the TWiki engine (Perl scripts).

Related Topics:

• TWikiPreferences has site-level preferences.
• TWikiUsers has a list of user topics. User topics can have optional user preferences.
• TWikiVariables has a list of common %VARIABLES%.
• TWikiAccessControl explains how to restrict access by users or groups.

http://bliss.biology.yale.edu/twiki/bin/view/Main The web for users, groups and offices. TWiki is a Web-Based Collaboration Platform for the Corporate World. en-us Copyright 2009, Peter Thoeny and contributing authors. Peter Thoeny [Peter@Thoeny.com] Peter Thoeny [Peter@Thoeny.com] TWiki TWiki.Main http://bliss.biology.yale.edu/twiki/bin/view/Main http://bliss.biology.yale.edu/twiki/pub/TWiki/TWikiLogos/twikilogo88x31.gif http://bliss.biology.yale.edu/twiki/bin/view/Main/WebStatistics Statistics for Main Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 8071 0 0 3877 ... 2009-11-22T07:37:00Z guest 1.490 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/WebStatistics http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/WebStatistics http://bliss.biology.yale.edu/twiki/bin/view/Main/JoeGlotz Name: Joe Glotz Email: Joe@joe.com Company Name: Company URL: Comment: Personal Preferences (details in TWIKIWEB .TWikiVariables) Horizontal size of text edit box ... 2006-12-04T18:07:00Z JoeGlotz 1.1 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/JoeGlotz http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/JoeGlotz http://bliss.biology.yale.edu/twiki/bin/view/Main/TWikiUsers List of TWiki users Please take the time and add yourself to the list. To do that fill out the form in TWIKIWEB .TWikiRegistration. This will create an account for ... 2006-12-04T18:07:00Z JoeGlotz 1.44 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/TWikiUsers http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/TWikiUsers http://bliss.biology.yale.edu/twiki/bin/view/Main/SupplementaryInformation4 Notes I recommend viewing the HTML alignnments. The stems and secondary structure are labeled at the bottom of the files. Pseudoknots are not currently annotated ... 2006-08-10T20:20:00Z JeffreyBarrick 1.2 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/SupplementaryInformation4 http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/SupplementaryInformation4 http://bliss.biology.yale.edu/twiki/bin/view/Main/WebHome What is BLISS? The BLISS website (Breaker Lab Intergenic Sequence Server) contains BLAST comparisons of intergenic regions (IGRs) from (mostly) microbial genomes ... 2005-11-06T23:12:00Z JeffreyBarrick 1.37 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/WebHome http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/WebHome http://bliss.biology.yale.edu/twiki/bin/view/Main/TWikiPreferences The site-level preferences are located in TWIKIWEB .TWikiPreferences Set ALLOWTOPICCHANGE MAINWEB .TWikiAdminGroup Set ALLOWTOPICRENAME MAINWEB .TWikiAdminGroup Main ... 2005-09-18T22:21:00Z JeffreyBarrick 1.1 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/TWikiPreferences http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/TWikiPreferences http://bliss.biology.yale.edu/twiki/bin/view/Main/SupplementaryInformation3 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR Supporting ... 2005-07-21T12:06:00Z JeffreyBarrick 1.3 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/SupplementaryInformation3 http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/SupplementaryInformation3 http://bliss.biology.yale.edu/twiki/bin/view/Main/AboutBliss About BLISS The BLISS website (Breaker Lab Intergenic Sequence Server) contains BLAST comparisons of intergenic regions (IGRs) from (mostly) microbial genomes. It ... 2005-03-23T19:17:00Z JeffreyBarrick 1.1 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/AboutBliss http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/AboutBliss http://bliss.biology.yale.edu/twiki/bin/view/Main/KenWickiser Name: Ken Wickiser Email: foo@foo.com Company Name: Company URL: Comment: Personal Preferences (details in TWIKIWEB .TWikiVariables) Horizontal size of text edit ... 2004-11-24T15:47:00Z KenWickiser 1.1 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/KenWickiser http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/KenWickiser http://bliss.biology.yale.edu/twiki/bin/view/Main/KristianLink Name: Kristian Link Email: linkk 1975@yahoo.com Company Name: Company URL: Comment: Personal Preferences (details in TWIKIWEB .TWikiVariables) Horizontal size of ... 2004-09-07T19:06:00Z KristianLink 1.1 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/KristianLink http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/KristianLink http://bliss.biology.yale.edu/twiki/bin/view/Main/ElizabethRegulski Name: Elizabeth Regulski Email: elizabeth.regulski@yale.edu Company Name: Company URL: Comment: Personal Preferences (details in TWIKIWEB .TWikiVariables) Horizontal ... 2004-07-28T19:10:00Z ElizabethRegulski 1.1 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/ElizabethRegulski http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/ElizabethRegulski http://bliss.biology.yale.edu/twiki/bin/view/Main/NoamRudnick Name: Noam Rudnick Email: bob@bob.com Company Name: Company URL: Comment: Personal Preferences (details in TWIKIWEB .TWikiVariables) Horizontal size of text edit ... 2004-06-17T20:32:00Z NoamRudnick 1.1 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/NoamRudnick http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/NoamRudnick http://bliss.biology.yale.edu/twiki/bin/view/Main/AlexBateman Name: Alex Bateman Email: foo@foo.com Company Name: Company URL: Comment: Personal Preferences (details in TWIKIWEB .TWikiVariables) Horizontal size of text edit ... 2004-04-23T21:01:00Z AlexBateman 1.1 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/AlexBateman http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/AlexBateman http://bliss.biology.yale.edu/twiki/bin/view/Main/RuedigerWelz Name: Ruediger Welz Email: fake@fake.com Company Name: Company URL: Comment: Personal Preferences (details in TWIKIWEB .TWikiVariables) Horizontal size of text edit ... 2004-04-11T20:19:00Z RuedigerWelz 1.1 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/RuedigerWelz http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/RuedigerWelz http://bliss.biology.yale.edu/twiki/bin/view/Main/SidneyAltman Name: Sidney Altman Email: foo@fake.com Company Name: Company URL: Comment: Personal Preferences (details in TWIKIWEB .TWikiVariables) Horizontal size of text edit ... 2004-03-31T15:37:00Z SidneyAltman 1.1 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/SidneyAltman http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/SidneyAltman http://bliss.biology.yale.edu/twiki/bin/view/Main/ZashaWeinberg Name: Zasha Weinberg Email: foo@foo.com Company Name: Company URL: Comment: Personal Preferences (details in TWIKIWEB .TWikiVariables) Horizontal size of text edit ... 2004-03-23T14:18:00Z ZashaWeinberg 1.1 updated major http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/ZashaWeinberg http://bliss.biology.yale.edu/twiki/bin/rdiff/Main/ZashaWeinberg

• Topic index: List of Main topics in alphabetical order.
  |All|A|B|C|D|E|F|G|H|I|J|K|L|M|N|O|P|Q|R|S|T|U|V|W|X|Y|Z|
  | All topics in BookView |

• Jump to topic: If you already know the name of the topic, enter the name of the topic at the second line of this page.

• WebChanges: Find out what topics in Main have changed recently.

• How to edit text:
  • Make changes to topics in GoodStyle,
  • Learn the TextFormattingRules, and
  • Have a look at the TextFormattingFAQ.

Statistics for Main Web

Notes:

• Do not edit this topic, it is updated automatically. (You can also force an update)
• TWikiDocumentation tells you how to enable the automatic updates of the statistics.
• Suggestion: You could archive this topic once a year and delete the previous year's statistics from the table.

• AboutBliss
• AdamRoth
• AlexBateman
• BenjaminBoese
• BrianTucker
• ElizabethRegulski
• FileAttachment
• GailEmilsson
• InbalJona
• IzabelaPuskarz
• JeffreyBarrick
• JenniferCollins
• JinsooLim
• JoeGlotz
• KeithCorbino
• KenWickiser
• KristianLink
• MarkLee
• MaumitaMandal
• MingCheah
• NarasimhanSudarsan
• NoamRudnick
• NobodyGroup
• RonaldBreaker
• RuedigerWelz
• ShingoNakamura
• SidneyAltman
• SupplementaryInformation1
• SupplementaryInformation3
• SupplementaryInformation4
• TWikiAdminGroup
• TWikiGroups
• TWikiGuest
• TWikiPreferences
• TWikiUsers
• TWikiVariables
• WadeWinkler
• WebChanges
• WebHome
• WebIndex
• WebNotify
• WebPreferences
• WebRss
• WebSearch
• WebStatistics
• WebTopicList
• ZashaWeinberg

See also the verbose WebIndex.

• Name: Zasha Weinberg
• Email: foo@foo.com
• Company Name:
• Company URL:
• Comment:

Personal Preferences (details in TWikiVariables)

• Horizontal size of text edit box:
  • Set EDITBOXWIDTH = 70
• Vertical size of text edit box:
  • Set EDITBOXHEIGHT = 17
• Style of text edit box. width: 99% for full window width (default), width: auto to disable.
  • Set EDITBOXSTYLE = width: 99%
• Optionally write protect your home page: (set it to your WikiName)
  • Set ALLOWTOPICCHANGE =

Related topics

• TWikiPreferences has site-level preferences of TWiki.
• WebPreferences has preferences of the TWiki.Main web.
• TWikiUsers has a list of other TWiki users.

Number of topics: 47