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Web report

Database of publicly available nucleotide sequences

Matthew Betts

  • Correspondence: Matthew Betts

Author Affiliations

Genome Biology 2000, 1:reports217  doi:10.1186/gb-2000-1-1-reports217


The electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2000/1/1/reports/217


Received:12 November 1999
Published:17 March 2000

© 2000 BioMed Central Ltd

Content

Publicly available nucleotide sequences, along with their associated annotations are available here. The data mostly come from the International Nucleotide Sequence Database Collaboration, made up of the European Bioinformatics Institute (responsible for the EMBL nucleotide sequence database), the National Center for Biotechnology Information (responsible for GenBank), and the DNA Databank of Japan. The members of this collaboration share their data on a daily basis. The GSDB compliments the data with additional tools for sequence searching and viewing. These data are searchable using BLAST sequence alignment programs (although the link was broken when I tried the site), a sequence retriever and viewer (programmed in Java), and more straightforward searches can be carried out, for example according to chromosome, organism and author. The different searches are interlinked, allowing the results of searches to be viewed easily in several different formats. Registration is required for use of the Java sequence viewer, but this is easy and free.

Navigation

Navigation was easy but it was sometimes unclear which of a variety of options was relevant to the problem in hand. The site may therefore require some getting used to but should prove useful with more experience.

Reporter's comments

Timeliness

This site is updated daily.

Best feature

There are several methods for searching the database.

Worst feature

The most powerful sequence retrieval and viewing tool on the site requires a Java plug-in program that appears to be available only for Windows 95/NT and Solaris (that is, not for the SGI that the site was reviewed on).

Wish list

A sequence viewer that runs on a wider variety of platforms would be useful.

Related websites

Nucleotide sequences are available from EMBL nucleotide sequence database database, GenBank and the DNA Databank of Japan.

Table of links

Assumptions made about all sites unless otherwise specified:
The site is free, in English and no registration is required. It is relatively quick to download, can be navigated by an 'intermediate' user, and no problems with connection were found. The site does not stipulate that any particular browser be used and no special software/plug-ins are required to view the site. There are relatively few gratuitous images and each page has its own URL, allowing it to be bookmarked.