Database of publicly available nucleotide sequences

Matthew Betts

doi:10.1186/gb-2000-1-1-reports217

Web report
Open Access
Published: 17 March 2000

Database of publicly available nucleotide sequences

Matthew Betts

Genome Biology volume 1, Article number: reports217 (2000) Cite this article

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Abstract

Publicly available nucleotide sequences, along with their associated annotations are available here.

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).