xBASE, a collection of online databases for bacterial comparative genomics

نویسندگان

  • Roy R. Chaudhuri
  • Mark J. Pallen
چکیده

The schema of the previously described Escherischia coli database coliBASE has been applied to a number of other bacterial taxa, under the collective name xBASE. The new databases include CampyDB for Campylobacter, Helicobacter and Wolinella; PseudoDB for pseudomonads; ClostriDB for clostridia; RhizoDB for Rhizobium and Sinorhizobium; and MycoDB, for Mycobacterium, Streptomyces and related organisms. The databases provide user friendly access to annotation and genome comparisons through a web-based graphical interface. Newly developed features include whole genome displays, 'painting' of genes according to properties such as GC content, a pattern search system to identify conserved motifs and batch BLAST searching of every protein encoded by a region. Examples of how the databases have been, and continue to be, used to generate hypotheses for subsequent laboratory investigation are presented. xBASE is available online at http://xbase.bham.ac.uk.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

xBASE2: a comprehensive resource for comparative bacterial genomics

xBASE is a genome database aimed at helping laboratory-based bacteriologists make best use of bacterial genome sequence data, with a particular emphasis on comparative genomics. The latest version, xBASE 2.0 (http://xbase.bham.ac.uk), now provides comprehensive coverage of all bacterial genomes and features an updated modularized backend and an improved user interface, which includes a taxonomy...

متن کامل

coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics

We have constructed coliBASE, a database for Escherichia coli, Shigella and Salmonella comparative genomics available online at http://colibase. bham.ac.uk. Unlike other E.coli databases, which focus on the laboratory model strain K12, coliBASE is intended to reflect the full diversity of E.coli and its relatives. The database contains comparative data including whole genome alignments and list...

متن کامل

The Qualitative Descriptive Approach in International Comparative Studies: Using Online Qualitative Surveys

International comparative studies constitute a highly valuable contribution to public policy research. Analysing different policy designs offers not only a mean of knowing the phenomenon itself but also gives us insightful clues on how to improve existing practices. Although much of the work carried out in this realm relies on quantitative appraisal of the data contained in international databa...

متن کامل

Annotation, comparison and databases for hundreds of bacterial genomes.

The multitude of bacterial genome sequences being determined has opened up a new field of research, that of comparative genomics. One role of bioinformatics is to assist biologists in the extraction of biological knowledge from this data flood. Software designed for the analysis and functional annotation of a single genome have, in consequence, evolved towards comparative genomics tools, bringi...

متن کامل

Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach

Among proteins, orthologs are defined as those that are derived by vertical descent from a single progenitor in the last common ancestor of their host organisms. Our goal is to compute a complete set of protein orthologs derived from all currently available complete bacterial and archaeal genomes. Traditional approaches typically rely on all-against-all BLAST searching which is prohibitively ex...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • Nucleic Acids Research

دوره 34  شماره 

صفحات  -

تاریخ انتشار 2006