The current version of KTUs [KTU4 (KTU ver. 4)] have been constructed with ESTs of tomato and wild relatives. ESTs were classified based on sequence homology with sequences of HTCs from Micro-Tom and BACs from the International Tomato Genome Sequencing (ITAG) Project (bacs.v782.seq). A set of ESTs classified with each HTC/BAC sequence were assembled into a unigene(s) by CAP3. ESTs without sequence homology to any HTC/BAC sequence were also assembled into unigenes. For each unigene, functional annotations from BLAST and InterProScan searches against public sequence databases, metabolic pathway searches in KEGG and LycoCyc, and detections of SNPs and SSRs were executed. With sequence comparisons between KTUs and the genome in ITAG, gene structures and structural variants among paralogues and cultivars have been also predicted. To provide the omics data, we have developed an integrated database 'TOMATOMICS', which also stores information from MiBASE and KaFTom, with layers of information from the bioinformatics analyses and manual curation.