New data

This page listed additions to the database, in reverse cronological order, since the initial version 11 release in September 2000. These listings are linked directly to placeholders on the appropriate pages.

May 21, 2001

• Because of large-scale demand, I have resumed the inclusion of secondary structures Adobe Acrobat files (.pdf) files. To start with, I am posting the old ones from last year. Over the next few weeks I will post new ones to fill in those that are new this year, and any left-overs. NOTE that I have no intenttion of updating these .pdf files; the up-to-date data is in the connect (.ct) and RNAML (.rnaml) files, which can be generated automatically. PDf files based on older structure models are designeted with . PDF files based on the up-to-date model are designatd with .
• Because PDf files are back, the "Stock Figures" page is no longer needed and has been removed. All of the links have been moved to the appropriate "Sequences & Structures" pages.
• Tom Hall has graduated and left the lab, and so no further updates or bug fixes are anticipated for BioEdit.
• and tags are no longer in use.
• I've simplified the organization of the 'sundry' pages - everything is now directly available from the Home Page.
• BioEdit has been moved to a new space for logistical reasons. Requests for the old BioEdit home page will be automatically redirected.

May 3, 2001

• Corrected the accession numbers for some of the nuclear RNase P RNAs (AF044326, AF044325, AF044331, AF044327, & AF044328), and fixed 2 errors in the sequence of the human nuclear RNA. These are marked in the database with . Please note that the alignments from both Chris Pitulle and Dan Frank contain two different sequence typographical 'mutations' each i n the human sequence. Thanks to Shawn Stricklin at Wash. U. for pointing these errors out.

March 15, 2001

• More sequences, from new genomes:
  • E. coli 0157:H7 EDL933 (RNA and protein)
  • E. coli 0157:H7 RIMD0509952 (RNA and protein)
  • Vibrio cholerae RNase P protein
  • Thermoplasma volcanum RNase P RNA
• The three-dimensional structure of the Staphylococcus aureus RNase P protein, from Spitzfaden, et al., 2000 JMB 295:105.
• The Bufo calamita nuclear RNase P RNA, from Chris Pitulle.
• A few of citations that show up a lot in the database have been updated from 'unpublished' to real citations, and a scattering of other citation updates:
  • Harris, et al., 2001 RNA 7:220
  • Yoon & Park, 2000 IJSEM 50:2021
  • Frank, et al., 2000 RNA 6:1895
  • Hocking, et al., 1999 Infect. Immun. 67:13
  • Takami et al, 1999 Biosci. Biotechnol. Biochem. 63:1134
  • Glass, et al., 2000 Nature 407:757
  • Ng, et al., 2000 PNAS PNAS 97:12176
  • Jarrous, et al., 1999 RNA 5:153

January 5, 2001

• A fairly elderly (1998) bacterial RNA alignment from Christian Massire, also available on his RNase P resource page, has been added to the database.
• New nuclear RNase P RNA sequences, structures, and alignment from Dan Frank, from his recent paper (Frank, et al., 2000 RNA 6:1895). This is the best available comprehensive nuclear RNA alignment, but is not as rigorous as the bacterial and archaeal alignments. I've taken the liberty of tuning this alignment up and this revised lignment has also been posted.
• As always, lots of improvements to BioEdit.

December 19, 2000

• The Sulfolobus solfataricus strain P2 RNase P RNA, from the complete but unpublished genome sequence.

December 14, 2000

• No new data, but lots of broken links fixed. The complete revamp of the site left about 1% of links broken or various reasons, and these have been repaired (one at a time!).

December 11, 2000

• Four additional bacterial RNase P RNA sequences from Royden Saah:
  • Azotobacter chroococcum
  • Pseudomonas stutzeri
  • Pseudomonas azotoformans
  • Pseudomonas putida

• Some additional bacterial RNase P RNA sequences from unfinished genome sequences have been added (Thanks to Christian Massire at Isis Pharmaceuticals for fishing these out):
  • Rhodopseudomonas palustris
  • Wolbachia sp
  • Nitrosomonas europaea
  • Desulfovibrio vulgaris
  • Geobacter sulfurreducens
  • Clostridium difficile
  • Carboxydothermus hydrogenoformans
  • Streptococcus mutans
  • Streptococcus equi
  • Bacillus anthracis
• The RNAML files have been updated to conform to some changes in the soon-to-be-released standard, from Russ Altman's lab. The posted connect & RNAML generator script has been updated to match.

What's new in release 11 - October 10, 2000

• Secondary structures are now provided in machine-readable files: connect (file.ct and file.ct2) and RNAML (file.rna). For more information on these file types, and how to use them, go to the Guide to data file types page.
• Premade drawings of secondary structures are now only available for representative RNAs, in Acrobat (.pdf) format only, on the "Stock images" page. PDF's for the rest of the RNAs will be posted if there is a demand for them, and as time allows.
• A simple Hypertext script, connect & RNAML generator, that generates connect and RNAML files from alignments has been added.
• As always, lots of improvements to BioEdit.
• A large number of new sequences have been added to the database.
• An additional column has been added to the listing to include, wherever possible, the strain a sequence comes from.
• I've sifted through the NCBI Taxonomy Browser & updated the names of organisms where appropriate.
• The bacterial type A, B, and C alignments, and the archaeal type A and M alignments have been substantially updated.
• Various minor and cosmetic changes throughout. Because of some reorganization of the site, old links into the site other than the "home" page may no longer be valid.

What's on the way:

• There are some genome sequences that need their RNase P RNA genes identified and posted.
• Although I've sifted through GenBank and the literature pretty hard collecting bacterial and archaeal RNase P RNA sequences, information on the eukaryotic RNAs, and all of the proteins, is in need of updating. This includes sequences, secondary structures, and alignments. This update is in progress.
• In the long run, if the RNAML/RiboML/Madison format is accepted by the RNA community, I will upgrade these from their current absolute minimal form to include much more info (e.g. citations, accession links, etc). If RNML becomes a real stadard, then the database will provide info predominantly in this format. In addition, the size of the database is stretching the limits of the usefulness of static HTML pages. I hope to convert everything over to a true searchable/sortable database format soon.