Scheme for detection of alternatively spliced transcripts. Each nrFLcDNA was searched against nrFLcDNA dataset, DFCI tomato TCs, and SGN tomato unigenes using BLASTN. Query nrFLcDNAs were designated as "target nrFLcDNAs." Sequences that matched the target nrFLcDNA by a threshold E-value of 1e-50 were grouped into a multi-sequence group. Intron detection was performed using the est2genome program by setting the target nrFLcDNA as "est" and member nrFLcDNA, unigene, or TC as "genome", and vice versa. Consequently, splicing variants were detected for 1,206 target nrFLcDNAs. Out of the 1,206 nrFLcDNAs, 388 nrFLcDNAs were aligned to SGN tomato BAC sequences (bacs.v374.seq.20081128091837). Classification of alternative splicing events was carried out manually using the 388 multi-sequence groups.