The alignment was constructed by comparing the upstream 300 nucleotides of B. subtilis
genes with those of orthologous genes of B. halodurans[1] and B. stearothermophilus[2].
A local alignment program LALIGN by W. Pearson[3] was used to detect locally conserved
regions and they were aligned with the B. subtilis sequence. Orthologous genes of
B. halodurans were supplied by I. Uchiyama and those of B. stearothermophilus were
obtained by finding the best hit counterparts from both genomes. Nucleotides conserved
across three species were highlighted except they belong to other coding regions.
[1] Takami H et al.(2000) Complete genome sequence of the alkaliphilic bacterium
Bacillus halodurans and genomic sequence comparison with Bacillus subtilis,
Nucleic Acids Res., in press.
[2] sequence data fetched from http://www.genome.ou.edu/bstearo.html
[3] downloaded from ftp://ftp.virginia.edu/pub/fasta