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The evidence datasets used included: gene prediction based on Genie [ 20] and GENSCAN [ 21]; Sim4 alignments to EST and full-insert cDNA sequencing reads derived from the BDGP cDNA project [ 29, 30], the earlier analysis of the Adh region [ 44], and dbEST (for example [ 16]); FlyBase ARGS [ 1]; GenBank/EMBL/DDBJ entries identified as Drosophila cDNA sequences [ 6, 7, 8, 9, 10, 11] and error report submissions to FlyBase [ 1, 2]; and BLASTX protein homology data.
The production of full-insert sequences from DGC cDNAs is summarized in Tables 1and 2. For DGCr1, clones were sized before sequencing.
Data were filtered using the Bioinformatics Output Parser (BOP), which also assembled all EST and full-insert cDNA sequence reads from a particular cDNA clone into a virtual assembly (BOP [ 12]).
The largest set of full-insert cDNA sequences came from the BDGP Drosophila Gene Collection (DGC) project [ 5, 29, 30].
The majority of the new genes show matches to EST (573; 71%) or full-insert cDNA sequences (273; 34%), indicating the importance of these alignments in identifying new genes missed by the