New GenoBase is released! 2015 January
| The GenoBase was originally created to support the E. coli K-12 genome project launched in 1989 in Japan. The original data were E. coli K-12 sequence entries in GenBank and their mapping onto the chromosome in printed format. The database was designed to facilitate classification of sequenced or yet to be sequenced chromosomal regions for efficient sequencing project management by the conventional sequencing method using Kohara ordered phage clones (Kohara, Y., et al., 1987).
Since the completion of the genome project, the purposes of the database had been shifted to accelerate functional analyses both for individual targeted gene and the global analyses of entire gene set. For this, we started to construct comprehensive experimental resources and those resources, such as plasmid clone and deletion strain libraries have been freely distributed as open resources to the communities.
The GenoBase provides information related to resources which we constructed and are constructing including quality control.
Please cite the following reference for the GenoBase: Y. Otsuka, et al. (2015) "GenoBase: comprehensive resource database of Escherichia coli K-12."Nucleic Acids Research, database issue.
|2014/12||Major update of GenoBase. The quality control of plasmid clone and deletion libraries were added.|
|The annotation of each of genes was replaced with the latest information from the GenBank entry of MG1655.|
|2014/12||Database tables of new Gateway entry clone library and the Barcode deletion lcollection were added.|
|2014/11||The database view of the GenoBase was newly designed for the quality control information of the ASKA libraries and Keio collection.|
|2009/01||Minor improvement of descriptions|
|2008/08||GenoBase version 7 created to display genome information for both E. coli K-12 MG1655 and E. coli K-12 W3110.|
|2007||Minor improvement of functionalities.|
|2006/05||Revision of ASKA clones has finished.|
|2006/05||Now the "Protein expression from ASKA clone" site is free from the restriction by password.Please feel free to look inside.|
|2006/05||GenoBase upgraded to version 6 updated to include new E. coli K-12 annotation information (M. Riley, T. Abe, M. B. Arnaud, M. B. Berlyn, F. R. Blattner, R. R. Chaudhuri, J. D. Glasner, H. Mori, T. Horiuchi, I. M. Keseler, T. Kosuge, N. T. Perna, G. Plunkett, III, K. E. Rudd, M. H. Serres, G. H. Thomas, N. R. Thomson, D. S. Wishart, and B. L. Wanner. Escherichia coli K-12: a cooperatively developed annotation snapshot - 2005. Nucleic Acids Res. 34 (1):1-9, 2006.) ECK Number (Ref.) was merged into the GenoBase data. The start position of genome sequence of W3110 was moved 336bp.|
|2006/04||Keio collection updated to reflect Riley et al. (2006) annotations (T. Baba, T. Ara, Y. Okumura, M. Hasegawa, Y. Takai, Y. Okumura, M. Baba, K. A. Datsenko, M. Tomita, B. L. Wanner, and H. Mori. Construction of Escherichia coli K-12 in-frame, single-gene knock-out mutants - the Keio collection. Molecular Systems Biology 10.1038:4100050, 2006.)|
|2006/04||ASKA clone library data updated to reflect Riley et al. (2006) annotations (M. Kitagawa, T. Ara, M. Arifuzzaman, T. Ioka-Nakamichi, E. Inamoto, H. Toyonaga, and H. Mori. Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 (5):291-299, 2005.)|
|2005/12||ORF annotations are updated according to Ref. Gene Names are matched with SuppleTableX of Ref. and updated annotation of E. coli K-12 is published. Ref.
Riley, Monica, Abe, Takashi, Arnaud, Martha B., Berlyn, Mary K.B., Blattner, Frederick R., Chaudhuri, Roy R., Glasner, Jeremy D., Horiuchi, Ta kashi, Keseler, Ingrid M., Kosuge, Takehide, Mori, Hirotada, Perna, Nicole T., Plunkett, Guy, III, Rudd, Kenneth E., Serres, Margrethe H., Tho mas, Gavin H., Thomson, Nicholas R., Wishart, David, Wanner, Barry L.
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005 Nucl. Acids Res. 2006 34: 1-9 http://nar.oxfordjournals.org/cgi/content/abstract/34/1/1
|2005/04||We have reopened the information of Kohara clones. The affected clones and comparison of old and new position information were listed in this file.|
|2005/03||Inconsistency of data in some Kohara clones We found a Inconsistency in our data of Kohara clones. This problem seemed to originate at the update of sequence informations especially at the time we had "corrected" the inversion of genome at rrn operons in our data. Now we partially closed the information about Kohara clones and correcting this problem.|
|2005/02||We have published the following works.
Tomoya Baba, Takeshi Ara, Miki Hasegawa, Yuki Takai, Yoshiko Okumura, Miki Baba, Kirill A Datsenko, Masaru Tomita, Barry L Wanner and Hirotada Mori
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection Molecular Systems Biology 2 doi:10.1038/msb4100050 http://www.nature.com/msb/journal/v2/n1/full/msb4100050.html
|2005/02||We have published the following works.
Masanari Kitagawa, Takeshi Ara, Mohammad Arifuzzaman, Tomoko Ioka-Nakamichi, Eiji Inamoto, Hiromi Toyonaga and Hirotada Mori,
Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Rese arch DNA Research 2005 12(5):291-299; doi:10.1093/dnares/dsi012 http://dnaresearch.oxfordjournals.org/cgi/content/abstract/12/5/291
|2004/05||GenoBase was upgraded to GenoBase5.|
|2004/05||Now you can request ASKA clones and Keio strains via this website.|
|2004/03||Second archive clone resequence project was fixed. Archive material ver1.0 and archi ve annotaion ver 1.3 was fixed. Recloning of archive clones using this list and W3110 ORF an notation ver1.3 is planning now.|
|2004/03||W3110 ORF annotation ver1.3 was fixed.|
|2003/11||E.coli ORF annotation meeting in USA. ORF annotation of MG1655 strain, EcoGene and GenoBase was compared.|
|2003/10||W3110 ORF annotation ver1.2 was fixed. Exact nucleotide point of rrnD-rrnE inversion in the strain was defined. JW5xxx is applied as a new ID system. Kohara clone of #619 conta ined extra IS5 copy at the terminal region (chimera clone), so the exact mapping to the geno me can not assigned. But it contaied malQ-envZ region which was confirmed by #619 transposon tag sequences. #532 was also estimated as a chimera clone which were connected by rrnE regi on. It contained purH-nfi region and partial yhdZ-yhdY region which was confirmed by #532 t ransposon tag sequences. #479, #480 and #515 terimal region were positioned in the W3110 der ivative (or kohara clone) specific tandem repeat region (Hesslinger and Sawers, DNA Seq. 199 8, 9(3), 183-188.). So their mapping is checked by using transposon tag sequences of each ko hara clone. Analysis of insertion sequences showed complex IS structure such as IS677::IS677 (IS677C and D) and IS911::IS30. Mapping of IS5 was checked by reference (Umeda and Ohtsubo, J Mol Biol. 1990, 213, 229-237.).|
|2003/05||W3110 complete genome sequence was fixed.|
|Our experimental results on DNA microarray and 2D proteome analyses were made available. Note that the "Somview" requires Java2 plug-in 1.3. The reference list of mutations can be searched for by the "SEARCH" option. In addition, direct SQL search can be made by using the "query by SQL" option. The latest database scheme design was made available.|
|2002/05||Primer tube label for archive clones were checked and re-labeled and re-arrayed. (Archive clone annotaion ver 1.2)|
|2002/02||Genobase was upgraded to GenoBase 4.0.|
|2001/09||Some of the ORF annotation lines and the information for some archive clones were updated. To develop a new data curration system, updating of ORF annotation was suspended for some time.|
|2001/09||W3110 ORF annotation ver1.1 and Archive clone annotaion ver 1.1 was updated. (compatible to old Takara microarray lot)|
|2001/04||"Top page design" was found to be not appropriately viewed by Netscape 4.7 on a system with Mac OS 8.5, though it was OK with Mac OS 9.1.|
|2001/04||GenBank format files of Kohara clones were made available from the menu by selecting "Advances search > Kohara-clone & ORF relation > [Select clone] > GenBank Format". The file contains the latest version of GenoBase annotation not present in the GenBank database and hence subject to changes (/product=, etc.).|
|2001/03||"N-end aa sequences" in the ORF-information page were released as our results of N-terminal sequencing of 2D-PAGE-separated protein spots of strain W3110.|
|2001/02||GenoBase was upgraded to GenoBase 3.0. Graphical interface for chromosomal location of genes could not be realized yet. "Repeat sequence data" of Genobase2 (IS, Chi, BIME, etc) were divided into two classes. JW numbers were renewed as id's for ORFs and RNAs. In addition, #_id used in GenoBase2 and old_id used in previous reports on W3110 genome sequence were continuously used. Also, "PCR_Takara_ID" adopted for E. coli DNA microarry chip numbering by Takara Co. Ltd were included. "Clone_name" such as "36-5G" indicates the plate number combined with its position of the entire archive clones stocked in 96 well plates. The top page graphics was found not to be correctly displayed by Netscape versions under 4.7 on a Macintosh, though the display of contetns was not affected.|
|2001/01||Construction of archive clones was completed.|
|2000/09||Link to GTOP (a database for protein structure at National Institute of Genetics) from the gene name upon keyword search was made available.|
|2000/07||The terminal positions of Kohara clones #233 and #441 were corrected. The right treminal end of Kohara clone #619 appeared problematic (reflecting a new IS insertion ?), and hence the clone was withdrawn.|
|2000/06||Bug report with IE: [ORF list] botton cannot be used correctly in JAVA view and link from the ORF table upon "function search" resulted in the display of the entire ORFs. With Netscape this functioned normally. On the other hand, the "function pull down menu" of IE upon ORF keyword search was convenient for users.|
|2000/05||The database top page was renewed. The official name of the database bacame "GenoBase".|
|2000/04||Major update of the database with the new sequence data and ORF annotation. A new policy concerning ORF annotation was proposed to include IS-encoded proteins and the relevant ORF data were incorporated. Consequently, the number of ORFs became 4388. Sequencing of the 70-100 min region of the W3110 genome was continued.|
|2000/03||Bug report: the amino acid sequence data for the 3 selenocystein-containing gene, fdnG, fdoG, fdhF were found to be incorrect and referrence to previous GenoBase pages was announced, although only changes of * to C (Sec) was necessary.|
|2000/03||A new web platform based on UNIX was established for GenoBase, since IE4/5 on Windows PC encountered troubles: some [LIST] button of the graphical JAVA interface to table information did not properly run, although Netscape on Windows PC did not show this problem.|
|2000/03||Archive clone annotaion ver 1.0 (include recloned clones in plate No 11 and 22)|
|2000/01||The whole dataset was decided to be transferred to a UNIX-based database system in the coming spring.|
|1999/11||The database system was renewed. GenoBase 2.0 was established with the status of archive clone development included.|
|1999/10||The ftp service page was updated.|
|1999/09||Some tRNA position data were updated.|
|1999/08||The data for Kohara clones #139, #152, #159 and #402 were updated.|
|1999/06||All BIME motifs (Y,Z,L,A,B) were searched for and incorporated into the database. All IS data were updated.|
|1999/03||An ORF database search interface was established at NAIST as GenoBase 1.5.|
|1999/03||The entire sequence data were updated (9902.seq.mod.S).|
|1999/01||The ends of some Kohara clones appeared to be problematic and the data for clones #479, #480 and #515 were retreated. Consequently, some ORF names on these Kohara clones were changed accordingly (such as #479 to #502, and #480/#515 to #516, etc).|
|1998/04||The E. coli nucleotide sequence data were made available to the public through GIB at the National Institute of Genetics.|
|1997/01||The genome sequencing of E. coli K12 strain MG1655 was completed.|
|1994/03||GenoBase 1.1 was published as a booklet.|
|The E. coli genome analysis project started in Japan.|