( r of the two unaligned sequenc...)The GeneZoo or the GeneJungle?

r of the two unaligned sequences is used to calculate the number of alignable bases. The number of alignable bases is simply the sum of the local alignment length plus the length of unaligned sequence flanking the local alignment. Of course, alignments of commonly repeated or low complexity sequences are discarded. The algorithm will not cluster sequences from different gene family members, since the untranslated regions tend not to align. In contrast, sequencing artifacts are ignored since they generally do not drop the percent identity below 96%. Our algorithm would place splice variants into different clusters; however since we only use the sequence contiguous to the poly-A tail to perform the clustering, splicing is not a significant factor. We could choose to ignore splice variants when clustering (Figure 2) by eliminating internally unpaired sequence from the computation of alignable length. However the algorithm we have chosen is more rigorous, and we rely instead on there being little splicing near the 3 ends.

Fig.1

We have also clustered our sequences together with 1.7 million human EST sequences that are included in the human UniGene Database (Build #116). Those clusters that contained a UniGene representative (Stratagene GeneZoo) were also compared with 41,472 sequence-verified IMAGE clones from Research Genetics, and 9,182 Unigem 2.0 clones from Incyte Genomics. Figure 1 shows that most clusters, except for those in Stratagenes GeneJungle, and except for 354 Incyte clones, fall within the 81,967 UniGene clusters. Interestingly, Incytes 9,182 Unigem clones collapse into 8,298 UniGene clusters when referenced against UniGene build #116, plus 354 non
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