- The Tomato Integrated Database -

TOMATOMICS is an integrated omics database for Solanum lycopersicum (tomato).

Major contents:

  1. Sequences of all ESTs, Micro-Tom full-length cDNAs, ITAG2.4 gene models, which are clustered by genomc position and sequence homology.
  2. Annotations for the sequences based on manual curation of scientific papers (knowledge-based functional description) and searches with BLAST, InterPro, and KEGG Pathway.)
  3. A genome browser showing genome structural annotation, SNP/InDel between Heinz 1706 and Micro-Tom, mapped RNA-seq reads, and so on.
  4. Gene expression and coexpression calculated using ITAG gene models.

Sequence search


Genome browser


BLAST


Query:
database :
program :

Citations


  • TOMATOMICS: A Web Database for Integrated Omics Information in Tomato.
    Kudo T., Kobayashi M., Terashima S., Katayama M., Ozaki S., Kanno M., Saito M., Yokoyama K., Ohyanagi H., Aoki K., Kubo Y., and Yano K., Plant Cell Physiol., 58(1):e8 (2017)
    [PubMed] [PCP]

  • Genome-Wide Analysis of Intraspecific DNA Polymorphism in ‘Micro-Tom’, a Model Cultivar of Tomato (Solanum lycopersicum).
    Kobayashi M., Nagasaki H., Garcia V., Just D., Bres C., Mauxion JP., Le Paslier MC., Brunel D., Suda K., Minakuchi Y., Toyoda A., Fujiyama A., Toyoshima H., Suzuki T., Igarashi K., Rothan C., Kaminuma E., Nakamura Y., Yano K., and Aoki K., Plant Cell Physiol., 55(2):445-454 (2014)
    [PubMed] [PCP]

Legacies


...

KaFTom

KaFTom provides information about Tomato full-length cDNA clones derived from Micro-Tom.

...

MiBASE

MiBASE provides information about Micro-Tom ESTs and Kazusa Tomato Unigenes ver.3 (KTU3) constructed from Micro-Tom ESTs and publicly available tomato ESTs.

News


2017-Jan-6 New

A TOMATOMICS paper has been published.
Kudo T., Kobayashi M., et al. "TOMATOMICS: A Web Database for Integrated Omics Information in Tomato."


2016-Oct

TOMATOMICS is officially released with TMCS genome annotation version 1.2.1.


2015-Aug

TOMATOMICS Updated


2015-Apr-7

Amino acid sequences of HTCs is downloadable. -> Download


2015-Feb-3

New tables are downloadble now. -> Download
(1) A table for Heinz 1706 transcript IDs in ITAG2.5, Micro-Tom names (EST,HTC), and INSDC Accession numbers
(2) A table for Heinz 1706 transcript IDs in ITAG2.5, SGN EST names, and INSDC Accession numbers


2011-Nov-28

"TOMATOMICS beta version" Release

'TOMATOMICS' has been developed and maintained by Bioinformatics Laboratory of Meiji University. Last Modified Feb. 9, 2017.