Gene Search

Vertebrate TimeCapsule

Vertebrate TimeCapsule (VTcap) is a publicly available gene database for investigations aimed at elucidating the evolutionary process of the vertebrate developmental systems. Sequence data derived from large-scale sequencing analyses in emerging model organisms are deposited. The detailed information of the analyses, the BLAST search and a sophisticated keyword search are available in this data base.

VTcap EST Project

The VTcap EST project aims to develop a gene database to represent evolution and development.
The goal of the project is to provide a fundamental database to investigate evolution and development by combination with other environmental data.

Image archive

VTcap version 1.0 is a first public edition of the database. This research article is published in Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2011 Aug 1. doi: 10.1002/jez.b.21427.

Takechi M, Takeuchi M, Ota KG, Nishimura O, Mochii M, Itomi K, Adachi N, Takahashi M, Fujimoto S, Tarui H, Okabe M, Aizawa S, Kuratani S.

Overview of the transcriptome profiles identified in hagfish, shark, and bichir: current issues arising from some nonmodel vertebrate taxa.

Gene Finding Tool

The Gene Finding Tool is a unique and effective EST based solution for bioinformatics analysis. The database can be searched not just by using the relevant gene sequence, but also by the use of arbitrary keywords. Additionally, a variety of related data is linked to the reference result, meaning that it is possible to perform advanced research by using minimum time and effort. BLAST reference, protein domain reference, redundancy, clustering, and assembling are all available in Gene Finding Tool.

Annotation - UniGene Analysis

UniGene is a system for automatically partitioning transcriptome sequences into a non-redundant set of clusters. Each UniGene cluster contains sequences that represent a unique gene. The goal of this technique is the same as UniGene of NCBI.

BLAST against VTcap ESTs

BLAST (The Basic Local Alignment Search Tool) that provide by NCBI finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to the EST databases and calculates the statistical significance of matches and can use not only EST data but also sequences extracted from any public resource.

Project Laboratories

Laboratory for Vertebrate Body Plan,

Laboratory for Evolutionary Morphology,

Genome Resouce and Analysis Unit,

RIKEN Center of Developmental Biology