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.
- 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
- 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
- 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.
- 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.
- More sequences, from new
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show up a lot in the database have been updated from 'unpublished'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.
- Takami et al, 1999 Biosci. Biotechnol.
- Glass, et al., 2000 Nature 407:757
- Ng, et al., 2000 PNAS PNAS 97:12176
- Jarrous, et al., 1999 RNA 5:153
- 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!).
- Four additional bacterial
RNase P RNA sequences from Royden Saah:
October 24, 2000
- 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):
- 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.
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
- 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
- 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.
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.
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