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Protein sets (proteomes) from the following pairs of complete genome sequences were compared in order to identify orthologous sequences: S. cerevisiae - S. pombe , S. cerevisiae - C. elegans , H. pylori strain 26695 - H. pylori strain J99, H. pylori strain 26695 - C. jejuni . Pairs of proteomes were compared using the BLASTP program [ 18 ] , with post-processing of results done using the SEALS package [ 19 ] . For each proteome, individual proteins were used as queries in BLASTP searches against the entire proteome of the other analyzed species (or strain).
Database searches of genomic sequences from Saccharomyces cerevisiae (yeast), Caenorhabditis elegans (roundworm), and Strongylocentrotus purpuratus (sea urchin) did not reveal genes encoding the TOX HMG signature sequence (data not shown).
Subsequent BAC end-sequencing and BLAST searches of the Tomato Gene Index identified BAC 9302 and 52M1 insert DNA ends nearest the telomere as containing genomic nucleotide sequence for two previously identified MESTs - TC92082 and TC98260, respectively.
We also did sequence-similarity searches using three different EF-hand proteins that have been characterized in Arabidopsis.
Database searches using Patternfind at the ISREC server were performed using parameters appropriate for short protein queries and were successful in identifying a human gene product, subunit p170 of eIF3 (Figure 3).