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Homologs recovered in the searches were collated and clustered at various thresholds of BLAST-bit-score to HSP-length ratios using the BLASTCLUST program [ 67].
At convergence, this search detected, in addition to the soluble guanylyl cyclases from the animals, several bacterial proteins, including certain methyl-accepting chemotaxis receptors from bacteria such as Desulfovibrio and Clostridium . Transitive searches initiated with the small bacterial proteins that entirely correspond to the N-terminal-most domain of the SGCs also recovered the same set of proteins as observed in the earlier search, with e <.01.
Although some of these searches converged prematurely, they consistently recovered true positives detected in the other searches with at least borderline statistical significance (e approximately 0.05-0.
EST datasets have been used recently to extract information on gene-expression levels [ 39 40 41 ] . The underlying assumption of such a 'digital northern' analysis is that the number of EST clones is proportional to the abundance of the mRNA used for constructing the library [ 42 ] . Most Arabidopsis EST collections are derived from non-normalized cDNA libraries, making them useful for this purpose [ 43 ] . We recorded the number of EST hits from the MIPS summary report link or by BLAST searches with the Arabidopsis EST database for each clone in our stress collection.
These searches captured 157 putative coding regions from 19 genes and 2 pseudogenes concentrated in the central 1200 Kb shown in detail in Figure 1with base pair 1 starting at the 5-prime end of FLJ12671 and ending 1 Kb centromeric to the 3-prime end of RPS10.