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The second objective was to sequence the duplex PCR products to verify their match to genes and chromosomes for which they were designed.
Triplet genes are genes with a mutual best match to genes in the other two subgenomes.
These EST sequences are submitted to databases and compared to all other sequences in the databases to see if they match to genes whose function has been determined.
The "Top 20 known genes" were taken from 36 transcripts of which 16 showed no match to genes of known function.
Of those 2749 Ginkgo biloba unigenes with matches to other plant genes, a subgroup of 256 unigenes had no corresponding match to genes in the angiosperm dataset.
Out of the 125,123 unigenes, 60,020 (49.5%) represented significant match to genes encoding proteins or putative function in at least one of these public databases (Table 2), whereas 50.5% unigenes could not be annotated to predicted coding regions with unknown functions in other species.
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The most established computational approaches to function detection primarily depend on homology matching to genes with known functions utilizing programs such as FASTA [4] and PSI-BLAST [5].
Additionally 298 TUGs had best, significant matches to genes from fungi (e.g Ajellomycetaceae, 53 hits) and 585 TUGs had best, significant matches to genes from plants.
All EST matches to genes were required to have >80% coverage over the EST sequence.
Therefore, the resulting ortholog clusters had to be matched to genes.
Around 25% of the tags that matched to genes are in antisense orientation (Table 3).
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