Ciona Resources

Tools

Ciona intestinalis Genome Browsers

a C. i. Genome Browser, customized by Dr. Maximilian Haeussler, displays various genomic and EST resouces including the recent KH (Kyoto Hoya) gene models.
(*the fastest due to BLAT search; in silico PCR is available; VISTA plots, polymorphisms, and multiple types of gene models are displayed, while links sometimes are broken)

JGI Ciona 2.0 /Ciona 1.0 /(The JGI Eukaryotic Genomics)
*v2.0 has a window for VISTA (Ci vs Cs)

Ensemble Ciona intestinalis Genome Browser/ Ensemble Project (home)

UCSC C.i. Genome Browser (tha BLAT is very fast to search sequences ! Other genomes of C. savignyi, Amphioxus, and Sea Urchin are also available.)

Ghost Ciona intestinalisGenome Browser/Kyoto Univ. (see below, too)
*it is based either on the JGI v1.0 assembly (Dehal et al. 2002) or newly assembly (with the KH models, Satou et al. 2008)

Primer design
Primer3

Comparative Genome
VISTA tools

LAGAN

Mobyle@Pasteur

Yutaka Satou lab. (Kyoto Univ.)

Ghost database
- Ciona cDNA resources
- Ciona chromosomes (guest access is available)
- Ciona genome browser (guest access is available)

Ciona intestinalis genome view

Trace Archive database Mega BLAST search

Ciona savignyi genome & cDNA resources
Ciona savignyi Database/ Broad Institute of MIT and Harvard

Pre-Ensemble Ciona savignyi/ Ensemble Project

Soft Ghost database /Kyoto Univ. (see the Ghost database)

DDBJ

Ciona intestinalis Developmental Genetics
Y. Sasakura's lab. (Shimoda, Tsukuba Univ., Japan)

Di Jiang's lab. (SARS, Norway)

Medline (Entrez, NCBI)
Nucleotide (Entrez, NCBI)
Protein (Entrez, NCBI)

Ciona Transgenic lines and AMAGEN platforms
JS Joly's team and his colleagues

Ciona savignyi

B. Smith's lab. (Santa Barbara, UCSB, USA)

Developmental Genetics (www.ascidiancenter.ucsb.edu)

Ascidian Network for In Situ Expression and Embryological Data
aniseed /Patrick Lemaire and the others

BLAST (NCBI)

Photographs of ascidian species
The Dutch Ascidians Homepage/ Arjan Gittenberger

BLAST (GenomeNet); KEGG etc.

Photographs of ascidian species
Ascidiacea.com/ Karen Sanamyan and the others

An e-mailing list
Tunicata List

Sequence Interpretation Tools

SRS, EBI

Genome Resources

Gene Ontology

Human (Ensembl)

Pfam

Flybase

InterPro

WormBase

SMART

Medaka Genome Database (M base)
/Hiroshi Mitani, Naruse Kiyoshi, Minoru Tanaka et al., (Univ. of Tokyo)

Grail