title: TOMATOMICS: A Web Database for Integrated Omics Information in Tomato.
abstract: Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
authors.forename: Toru
authors.initials: T
authors.lastname: Kudo
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
authors.forename: Masaaki
authors.initials: M
authors.lastname: Kobayashi
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
authors.forename: Shin
authors.initials: S
authors.lastname: Terashima
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
authors.forename: Minami
authors.initials: M
authors.lastname: Katayama
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
authors.forename: Soichi
authors.initials: S
authors.lastname: Ozaki
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
authors.forename: Maasa
authors.initials: M
authors.lastname: Kanno
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
authors.forename: Misa
authors.initials: M
authors.lastname: Saito
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Yokoyama
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.|King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia.
authors.forename: Hajime
authors.initials: H
authors.lastname: Ohyanagi
authors.affiliation: Graduate School of Life and Environmental Sciences, Osaka Prefecture University,  Gakuen-cho, Naka-ku, Sakai, Japan.
authors.forename: Koh
authors.initials: K
authors.lastname: Aoki
authors.affiliation: Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
authors.forename: Yasutaka
authors.initials: Y
authors.lastname: Kubo
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yano
mesh_terms: D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary / Q000235:genetics*; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D020407:Internet; D018551:Solanum lycopersicum / Q000235:genetics*; D009154:Mutation; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics
chemical_list: D018076:DNA, Complementary
keywords: Database; Genome; Micro-Tom; Solanum lycopersicum (tomato); Transcriptome