BIOINF 03-002 Supplemental Material

Surveying Phylogenetic Footprints in Large Gene Clusters: Applications to Hox Cluster Duplications

Sonja J. Prohaska, Claudia Fried, Christoph Flamm, Günter P. Wagner, Peter F. Stadler

Hox Gene Identities

Takifugu rubripes sequences were obtained by Blast searches against version 3.0 of the Fugu database: http://genome.jgi-psf.org/fugu6/fugu6.home.html.
In order to prove the assembly of the genes clustalW alignments against known Hox proteins of different species were build.

Table 1 shows the percent identity obtained by clustalW for Takifugu rubripes. At the end of the table the best hits are listed and the last line indicate the proposed gene.

Table 2 shows analogous data for the Danio rerio Ca cluster. This sequence is a composite of zK81P22.00296(r.c.) + 3084*N + zK81P22.01466(r.c.) + 2956*N + zK81P22.00552 of the Sanger site http://www.sanger.ac.uk/Projects/D_rerio/ (download 12.1.03).