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Web report

Little weed: Arabidopsis genomic and related data

Penny Webb

Genome Biology 2001, 2:reports2010  doi:10.1186/gb-2001-2-9-reports2010

The electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2001/2/9/reports/2010


Received:24 July 2001
Published:29 August 2001

© 2001 BioMed Central Ltd

Content

The Arabidopsis Information Resource (TAIR) provides a collection of tools, links and news for researchers working with Arabidopsis thaliana. The Arabidopsis genome annotated sequence was published late last year. The recently redesigned TAIR site contains genome sequence initially annotated by AGI (The Arabidopsis Genome Initiative) that is currently in the process of being reannotated, with an update list appearing every few months. A plethora of tools and datasets is available for data searching and analysis in many different ways. The site provides extensive links, including those to other Arabidopsis databases, stock centers and plant biology resources. Sequence analysis, nomenclature and bioinformatic links are quite comprehensive, and there is also a good selection of plant microarray information. Beta versions of TAIR map viewer and TAIR database are currently in place. Judging by the pages explaining progress and what is to come, there are still many features in store for this site.

Navigation

The homepage consists of a list of categories followed by headings for the contents of each page, which makes it easy to select the page required. It is not as pretty as the old homepage, but is more functional for quick access. Navigation menus and search boxes are at the top of the main pages but do not appear on many of the results pages.

Reporter's comments

Timeliness

The last update for the website was 17 July 2001. The site is updated regularly with a 'breaking news' feature on the several categories on the home page.

Best feature

Gene Hunter searches nine different sites for relevant information about a gene. If you select your search term carefully, Gene Hunter retrieves the available information from all sites despite each of the site's idiosyncrasies regarding search-term nomenclature.

Worst feature

If you click a link to MapViewer from the Genetic Marker Object databox, or vice versa, when both frames are already open the content of the frame is updated but the window you have selected confusingly stays in the background.

Wish list

It would useful to have the sequence map resolved and accessible down to nucleotide level with features marked.

Related websites

Other Arabidopsis genome resources include the TIGR Arabidopsis thaliana Database, Department of Plant Gene Research at the Kazusa DNA Research Institute, the MIPS Arabidopsis thaliana Database (MATDB) and the Database of Arabidopsis thaliana Annotation (DAtA).

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.