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Fugu: the small genome of a puffed-up fish

Aengus Stewart

  • Correspondence: Aengus Stewart

Author affiliations

Citation and License

Genome Biology 2000, 1:reports210  doi:10.1186/gb-2000-1-1-reports210


The electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2000/1/1/reports/210


Received:23 October 1999
Published:17 March 2000

© 2000 BioMed Central Ltd

Content

The puffer fish Fugu rubripes is perhaps better known as a Japanese delicacy, but its gene-rich, relatively small genome makes the puffer fish a suitable vertebrate for comparative mapping. This site contains all the data currently available from the Fugu comparative mapping project: its background, aims and origin, and 'everything you ever wanted to know about puffer fish'. Search tools are provided that allow interrogation of the sequence data by keyword or BLAST search, and it is also possible to retrieve specific information on cosmids or clones for both genomic and cDNA sequences.

Navigation

Links are clear and the data are cross-linked, providing easy movement up, down and across the data tree and making the site straightforward and simple to use. Searching and retrieving data is relatively painless. The front page contains links to the rest of the HGMP-RC, and there are links to cited references in PubMed. A feedback page is provided, but it is not Fugu specific and the site is fairly minimalist.

Reporter's comments

Timeliness

Unfortunately, no date stamp is provided, making it difficult to determine how up to date the site is.

Best feature

The site is simple, with no-nonsense access to the available data and no unnecessary images or other web frippery.

Worst feature

There is little explanation and this site assumes a substantial degree of familiarity from the user. The statistics page, although warning that the links on the page may take some time, returns errors, as do the 'Detailed analysis of BLAST results' links from the 'Clone details' pages. There are no recipes for preparing puffer fish, although details of its poison can be found from links on the site.

Wish list

A summary table containing the current state of play would be a nice addition to the front page, as would a little more explanation in general. Correction of bad links is needed. Rather than displaying the database information in the browser window, a download option should be offered.

Related websites

There are quite a number of vertebrate genomic sequence/mapping sites, of which Zebrafish information network and Xenopus molecular marker resource are two examples.

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.