August 2, '01: After
a long silence (as we obtained funds to continue this project) this website
has now been updated to reflect some significant changes as we move into
this project's next phase. PseudoCAP will now be taking over the www.pseudomonas.com
website and will be coordinating efforts to continually update the Pseudomonas
aeruginosa genome annotation. The P. aeruginosa Genome Project
website will be changing significantly to reflect these changes and reflect
further development of the database flexibility. This new phase of the
project was made possible through funds obtained from the U.S. Cystic
Fibrosis Foundation.
October 12, '00: A link to the P. aeruginosa genome paper article as referenced in PubMed, was added to the main web site page now that such links are available. Note that the current PubMed reference (no longer a "Medline record in progress") is currently missing the names of five authors, however the NLM has been notified of this and so this will likely be fixed shortly. A link has also been supplied to a letter published in the same issue of Nature that briefly describes the PseudoCAP project, and suggests how a version of this method may be useful for future genome projects. Note also that the special issue of Microbiology devoted to Pseudomonas is now available (October 2000 issue), however I'll hold off from creating a link to this issue until it is archived.
September 17, '00: A link to info about the special issue of Microbiology devoted to Pseudomonas has been added under the section of this website which lists Pseudomonas genome analysis resources.
September 15, '00: Aspects of this site updated, including the addition of more resources under the Pseudomonas genome analysis resources. Note that a number of new tools have been made available now through the Pseudomonas Genome Project website, that include retireval of a portion of sequence and a flatfile of all annotations (a table summarizing the "annotation database").
August 31, '00: We are pleased to announce after a long silence on this webpage that the first complete Pseudomonas aeruginosa genome sequence has been published (see the August 31st issue of Nature)! Due to embargo rules, we were unable to post information on this website, however now we can point you to the new Pseudomonas Genome website for all the published information. Please note that the annotation information on the PseudoCAP server represents annotations submitted by participants using older versions of the genome sequence and should not be construed as the most up to date annotations. For the most up to date information, please see the Pseudomonas Genome website. We would like to take this time to thank all PseudoCAP participants for their involvement in the phase of the project. Now that the publication is out, we can move on to the next stage of further improving this annotation...
August 12, '99: The PseudoCAP annotations are now available for project participants to view from the PseudoCAP file server. Annotations are available both as web pages that may be viewed, showing their original submission format, and as a summary table that may be downloaded. There is now a total of 1741 separate annotations that have been submitted.
July 22, '99: A file containing a list of ORFs for the July 15th sequence version, along with BLASTP top hits against the nr database, is now available for download on the PseudoCAP file server or at the PathoGenesis ftp site (i.e., it is publicly available). A few additional points to clarify: The PseudoCAP annotations will be released shortly, but only to PseudoCAP participants. Participants, please note that for each annotation the contig range for both the March 15 and July 15, 1999 sequence release will be made available. You may also wish to note that there was a problem on July 15th with performing analyses of P. aeruginosa sequence using NCBI's unfinished microbial genomes BLAST server. This problem is now fixed and had occurred on July 15th only. You will want to discard any BLAST analyses performed on that day - particularly those where the database size is indicated on the output as "4,633,595 total letters" instead of the correct total of "6,261,175 total letters".
July 16, '99: The list of all participants has been updated. Participants, please let me know if there are any corrections to made to this list.
July 15, '99: The new sequence version comprising a single contig has been released by the Pseudomonas Genome Project. Please note that this is not the final sequence version and there are gaps and rearrangements that are in the process of being resolved. You may also wish to note that this will be the final sequence version released by the genome project before publication of the complete genome sequence. Annotation data will be forthcoming soon (PseudoCAP participants will be contacted by email).
July 14, '99: The web address for the PseudoCAP web site has now been changed to http://www.cmdr.ubc.ca/bobh/PAAP.htm. All related pages have changed accordingly (i.e. the word "interchange" in the domain name is now "cmdr"). This was done to avoid problems such as what occurred March 27th (see below). While at present the old web address will still work, please change your bookmarks and links from your own web pages accordingly.
May 19, '99: I (Fiona Brinkman) will be away until June 5th and so will not be able to respond to any emails sent over the next two and half weeks until I return.
May 15, '99: All of the PseudoCAP annotation submissions have now been processed and integrated into the Pseudomonas Genome Project's database (phew - there was a lot of them!). Another "pass" of the genome is now being performed by the Genome Project annotators and the PseudoCAP committee is reviewing the annotations. A collection of all PseudoCAP annotations will eventually be made available to all participants - participants will be contacted by email when this is available from the PseudoCAP File Server. If any participant does not wish their annotations to be released to all participants, please contact me at fiona@cmdr.ubc.ca.
PseudoCAP statistics: We have received a total of 1622 separate gene annotations, which covers over a quarter of the estimated ORFs in the genome (or a higher percentage if you consider this number as a proportion of only the annotatable ORFs). Annotations were received from approximately 80% of the initial participants - an impressive participation rate given that this work was performed on a volunteer basis by most laboratories. We commend all participants for their impressive contributions to this important work.
April 8,'99: Many thanks to all of the participants who have submitted annotations! Many submissions were received in the past two weeks and the annotations are currently being processed. We will email participants shortly with some statistics (ie., total number of submissions we received etc...), and provide an indication of what will happen next. Some of this information will also be posted here for your reference.
March 27-28, '99: The PseudoCAP web site was down. Our apologies for any inconvenience this may have caused. Due to this problem, we have extended the deadline for submission of annotations for the first complete-pass annotation to April 6th, 1999, from March 31st.
March 15, '99: Correction of the March 14, 1999 statement made below. All 53 contigs for the Pseudomonas Genome Project's March 15, 1999 sequence release are available now from the Pseudomonas Genome Project's web page. However, please note that only contigs 42 to 53 are over 2 kb and so analysis is focused on them. If you wish to recieve analyses of the "under 2 kb" data, please contact fiona@cmdr.ubc.ca.
March 14, '99: BLAST and ORF analyses for the March 15th, 1999 sequence data are now available on the PseudoCAP File Server. Note that there are only 12 contigs for this data release in total, however they are numbered contig 42 to 53. Please also note that ORF I.D. numbers for this new analysis are new numbers that are consecutive to any previous analyses. These numbers therefore can be used to specify a particular sequence or gene from this particular data release. These March 15th analyses are similar to other analyses, though the BLASTX analysis has not been included (due to lack of interest in the file - please let us know if you are interested in receiving it) and there has been one minor change in the BLASTP file (no "hit order" column is indicated).
March 3, '99: Informed participants that the deadline for submission of annotations, for inclusion in the first complete-pass annotation, is March 31st, 1999. Please email Bob Hancock if you were not informed of this and should have been.
January 17, '99: Added the file PaALLRESULTS1298.exe to the PseudoCAP file server. This file is a self-extracting executable containing all four files of data for the analysis of the December 15th, '98 sequence release. A reminder that this file can be used only by those who have Excel for Windows 5.0 or greater, and Windows 95/NT or greater. Others without this software, or who have a slow internet connection, can download the same data as compressed tab-delimited text files that are also present on the file server.
January 15, '99: Emailed participants to inform them of the new data release. If you are a participant and did not receive this email, or are interested in participating, please contact us.
January 14, '99:On the PseudoCAP File Server the "PaBLASTP1298allORFs" file was found to have an error in it that would lead to difficulty importing the data into a spreadsheet program (though the data itself was OK). This file was deleted and a new version of this file was created and named "PaBLASTP1298fixed" and is now available for downloading from the PseudoCAP File Server. The file "PaAllRESULTS1298fixed" was also created which contains this corrected file.
January 12, '99:BLAST and ORF analyses for the December 15th, 98 data are now available on the PseudoCAP File Server. Please note that ORF I.D. numbers for this new analysis are essentially new numbers that are consecutive to the previous analysis (i.e., The same number is not used throughout different data releases for a given region of sequence since this creates logistical problems). However, since these numbers are consecutive, ORF I.D.'s can be used to specify a particular sequence/gene from a particular data release.
These December 15th analyses are similar to the September 15th analyses with the following minor changes:
January 11, '99: This "what's new"
section of the PseudoCAP web site created!