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Published online 11 May 2004

Nucleic Acids Research, 2004, Vol. 32, No. 8 2618-2622
© 2004 Oxford University Press

A Fugu–Human Genome Synteny Viewer: web software for graphical display and annotation reports of synteny between Fugu genomic sequence and human genes

Mark Halling-Brown, Clare Sansom, David S. Moss, Greg Elgar1 and Yvonne J. K. Edwards*,1

School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK and 1 MRC Rosalind Franklin Centre for Genomics Research, Genome Campus, Cambridge CB10 1SB, UK

*To whom correspondence should be addressed. Tel: +44 1223 494531; Fax: +44 1223 494512; Email: yjedward{at}rfcgr.mrc.ac.uk

Received February 17, 2004; Revised March 30, 2004; Accepted April 7, 2004

A web server has been developed to access annotation and graphical reports of synteny and gene order between the Fugu genome and human genes. In this system, the assembled Fugu genomic sequences (also known as scaffolds) are annotated. The annotations for each Fugu scaffold are computed, stored and made publicly available. The annotations describe matches to human homologous genes. For each significant human gene match on the Fugu scaffold, the corresponding human chromosome map and measures of the significance of each match are given. The web-based server provides public access to these annotations and graphical displays of the results. The user is provided with a selection of views including a chromosome-colour-coded image and a table containing the details of the matches. The Fugu–Human Genome Synteny Viewer has been tested by comparing results with examples from a paper that includes a study of transcription factors, Fos and Jun encoding regions. The Fugu–human genome synteny views are available for each Fugu scaffold through the clonesearch web page located at the Fugu Genomics website (http://fugu.rfcgr.mrc.ac.uk/).


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