大肠杆菌K12 DNA序列汇编：交互式数据库ECD和ECDC的描述（1996年更新）

Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC (update 1996).

作者信息

Kröger M, Wahl R

机构信息

Institut für Mikrobiologie und Molekularbiologie, Fachbereich Biologie, Justus-Liebig-Universität Giessen, Frankfurter Strasse 107, D-35392 Giessen, Germany.

出版信息

Nucleic Acids Res. 1997 Jan 1;25(1):39-42. doi: 10.1093/nar/25.1.39.

DOI:10.1093/nar/25.1.39

PMID:9016501

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC146385/

Abstract

We have compiled the DNA sequence data forEscherichia coliavailable from the GenBank and EMBL data libraries and independently from the literature. We provide the most definitive version of the ECDEscherichia colidatabase now exclusively via the World Wide Web System: http://susi.bio.uni-giessen.de/usr/local/www/ html/ecdc.html . Our database encloses an assembled set of contiguous sequences. Each of these contigs compiles all available sequence information, including those derived from a variety of elder sequences. The organisation of the database allows precise physical location of each individual gene or regulatory region, even taking into consideration discrepancies in nomenclature. The WWW program allows to branch into the original EMBL and SWISSPROT datafiles. A number of links to other WWW servers is provided. A FASTA and BLAST search may be performed online. Besides the WWW format a flat file version may be obtained via ftp. The ftp version may also be obtained from the EMBL data library as part of the CD-ROM issue of the EMBL sequence database, which is released and updated every 3 months. After deletion of all detected overlaps a total of 3 588 706 individual bp has been determined up to the end of September 1996. This corresponds to a total of 77.09% of the entire E.coli chromosome consisting of approximately 4655 kb. About 479 kb (10.3%) are additionally available from Kyoto (Japan). Another 94 kb (2%) are available, but mapping has not been confirmed. Thus the total may have reached 89.4%.

摘要

我们已从GenBank和EMBL数据库以及独立的文献中收集了大肠杆菌的DNA序列数据。现在，我们通过万维网系统（http://susi.bio.uni-giessen.de/usr/local/www/html/ecdc.html）独家提供最权威的大肠杆菌数据库（ECDC）版本。我们的数据库包含一组组装好的连续序列。每个重叠群都汇集了所有可用的序列信息，包括那些从各种早期序列衍生而来的信息。数据库的组织方式使得即使考虑到命名法上的差异，也能精确确定每个基因或调控区域的物理位置。万维网程序允许链接到原始的EMBL和SWISSPROT数据文件。还提供了许多到其他万维网服务器的链接。可以在线进行FASTA和BLAST搜索。除了万维网格式，还可以通过ftp获得文本文件版本。该ftp版本也可以从EMBL数据库作为EMBL序列数据库光盘版的一部分获得，该光盘版每3个月发布和更新一次。在删除所有检测到的重叠部分后，截至1996年9月底，已确定了总共3588706个碱基对。这相当于整个大肠杆菌染色体（约4655kb）的77.09%。另外，约479kb（10.3%）可从日本京都获得。还有94kb（2%）可用，但图谱尚未得到确认。因此，总数可能已达到89.4%。