Post-Genomics Blog

Forging a connection between research and clinical applications.

Latest Fugu Assembly Available in Genome Browser

11 April 2007
Latest Fugu Assembly Available in Genome Browser

The UCSC Genome Browser now includes the latest release of the Fugu genome. The v4.0 whole genome shotgun assembly (Oct. 2004, UCSC fr2) was provided by the US DOE Joint Genome Institute (JGI) as part of the International Fugu Genome Consortium led by the JGI and the Singapore Institute of Molecular and Cell Biology (IMCB).

This version has been sequenced to approximately 8.5X coverage. The assembly contains 7,213 scaffolds covering 393,312,790 bp. The UCSC browser displays the scaffolds on the virtual chromosome chrUn with gaps of 1,000 bp between scaffolds. The scaffolds range in size from 2,223 bp to 7,245,445 bp. Fifty percent of the sequence (196,648,171 bp) is contained within 125 scaffolds of size 858,115 or greater (N50). The Fugu mitochondrial sequence is also available as the virtual chromosome chrM (GenBank accession: NC_004299.1).

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. These data have been freely provided by the JGI for use in the UCSC Genome Browser.

Many thanks to the JGI, IMCB, and the International Fugu Genome Consortium for the assembly data. The UCSC Fugu Genome Browser was produced by Cory McClean, Hiram Clawson, Ann Zweig, and Donna Karolchik. The annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

The SOL Genomics Network

sol genomics network
“The SOL Genomics Network (SGN) is a website dedicated to the biology of the Solanaceae family which includes a large number of closely related and many agronomically important species such as tomato, potato, tobacco, eggplant, pepper, and the ornamental Petunia hybrida.
SGN is part of the International Solanaceae Initiative (SOL), which has the long-term goal of creating a network of resources and information to address key questions in plant adaptation and diversification.�

Stanford Genomic Resources

Stanford Genomic Resources
“Hyperlinks to systematic analysis projects, resources, laboratories, and departments at Stanford University. Maintained by the Saccharomyces Genome Database within the Department of Genetics part of the School of Medicine.”

ExPASy Proteomics tools

The ExPASy Proteomics Server
“The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE” and provides access to numerous databases, tools, software packages, and other information.

Tips, Tutorials, and Terminology

Tutorials and terminology resources from the Human Genome Project
“The following tutorials are targeted to first-time users of some of the bioinformatics resources described in Genome Database Guide. Each tutorial includes step-by-step instructions and screen shots covering basic skills needed to use each Web site. Links to help files and other Web-based instructions for learning more about the different features of each bioinformatic tool are also provided.”

NCI Genomics and Bioinformatics Group Microarray Tools

The Microlarray Tools of the NCI Genomics and Bioinformatics Group:
AbMiner
MatchMiner
GoMiner
HT-GoMiner
SmudgeMiner
MedMiner
CIMminer

BITOLA – Biomedical Discovery Support System

BITOLA – Biomedical Discovery Support System
created by Dimitar Hristovski and Borut Peterlin
“BITOLA is an interactive literature-based biomedical discovery support system. The purpose of the system is to help the biomedical researchers make new discoveries by discovering potentially new relations between biomedical concepts. The set of concepts currently contains MeSH (Medical Subject Heading), which is used to index Medline, and around 22000 human genes from HUGO and LocusLink. The potentially new relations are discovered by mining the Medline database (currently around 11000000 citations from 1966 to end of 2001).
To make the system more suitable for disease candidate-gene discovery and to decrease the number of candidate relations, we integrated background knowledge about the chromosomal location of the starting disease as well as the chromosomal location of the candidate genes from resources such as LocusLink, HUGO and OMIM. The BITOLA system can also be used as an alternative way of searching the Medline database.”

Databases, Toolbox, Submissions, and Downloads

EMBL-EBI European Bioinformatics Institute Databases, Toolbox, Submissions, and Downloads.

Data Mining

Tools for Data Mining from the National Center for Biotechnology Information

Environmental Genomics Data Catalogue

EnvBase: The NERC Environmental Genomics Data Catalogue from The NERC Environmental Bioinformatics Centre.

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