How Informatics Unites Teams

... In La Jolla, a group led by Jackson Wan, PhD, director of bioinformatics, develops most of the global bioinformatics and related IT software... Click here to read more about the story.

iProClass Database

The iProClass is an integrated resource that provides comprehensive family relationships and structural functional features of proteins. It currently consists of non-redundant PIR and SwissProt/TrEMBL proteins organized with more than 36,000 PIR superfamilies, 145,300 families, 7670 domains, 1300 motifs, 280 post-translational modification sites, and links to over 90 biological databases.
The iProClass is implemented in Oracle 8i system, and can support protein sequence annotation and genomic/proteomic research. Click here to visit iProClass.

OGRe Database Takes 5th Position on MSN!

OGRe database takes 5th position on MSN. Check it out Here. The fouth position was taken by a page from my personal website at this moment.

OGRe Database Takes Second Position on Yahoo!

OGRe Database Takes Second Position on Yahoo! Check it out HERE.

OGRe Database Takes Second Position on Google!

OGRe Database Takes Second Position on Google! Believe or not, if you google "ogre database", you'll find that OGRe is at the second position on Google now. You can click here to take a look. I did this site search engine optimization (SEO) and submited it google :=). It's prety cool.

OGRe Database On The Fly

Organellar Genome Retrieval(OGRe) database was originally designed based on a collection of complete metazoan mitochondrial genomes by Dr. Higgs group in Bioinformatics at the University of Manchester. Since its first release in 2003, it has been updated several times. First, the host of OGRe database has been relocated to McMaster University and the World Wide Web address of OGRe has been set up permanently as http://ogre.mcmaster.ca. Second, the amount of stored data has increased significantly from 261 to 473 metazoan organisms and all related information has been updated. Third, new graphic tools that allow the manipulation of base frequencies, codon frequencies and amino acid frequencies for any set of selected species from OGRe have been developed. Lastly, several improvements that provide a better layout and make OGRe easy to navigate have taken place. For detail, check it out here. BTW, I was the major designer of the second version of OGRe.

LINKS: Connect to Bioinformatics

This directory of bioinformatics Web sites, compiled by Francis Ouellette's group at the University of British Columbia in Canada, features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee.

GENSAT : Gene Expression Nervous System Atlas

GENSAT Methods: "The GENSAT database contains a gene expression atlas of the central nervous system of the mouse based on bacterial artificial chromosomes (BACs). In each of the BAC transgenic vectors, endogenous protein coding sequences have been replaced by sequences encoding the EGFP reporter gene. As in any gene replacement experiment, the stability of the reporter gene can vary somewhat from the endogenous gene. Thus these results measure the relative rates of transcription for each gene; they are not a direct measure of mRNA accumulation or of protein abundance for the endogenous gene products. Furthermore, the enhanced sensitivity of reporter gene assays, particularly in BAC lines carrying multiple copies of the BAC transgene, may allow detection of sites of expression that are not evident in situ hybridization experiments.
This database contains histological data from given BAC transgenic mouse lines at three developmental stages - embryonic day 15.5 (E15.5), postnatal day 7 (P7) and adult; in all cases the data represent results of multiple transgenic lines. EGFP is visualized by staining with an anti-EGFP antibody using the DAB method, or by confocal microscopy of unstained tissue sections. "

DATABASE: A Visual Take on Proteins

There was a paper, DATABASE: A Visual Take on Proteins, published on Science -- 304 (5676): 1421d. Here is its summary "The enzyme DNA polymerase is a molecular Xerox machine, cranking out copies of DNA before a cell divides. To investigate the architecture and activity of DNA polymerase or nearly 27,000 other proteins and nucleic acids, dig into the recently revamped PDBsum, created by Roman Laskowski of the European Bioinformatics Institute in Hinxton, U.K. The database provides visual synopses of structural and functional information stashed in the Protein Data Bank repository. But the site also supplies additional info. For instance, you can highlight structures such as helices and sheets and diagram the interactions between a protein and other molecules or metals. If enzymes are your bag, the linked Enzyme Structures Database houses data on some 12,000 of the proteins, organized by reaction mechanism. "

I Am So Exciting For My New Bioinformatics Blog

After working for a while, I finally got my new bioinformatics blog running. It'll be a little corner of mine on the Internet focus on bioinformatics. As a bioinformatician, I know I have lots to learn, I would like to share with world for what I learn about bioinformatics here with a blog. Since English is not my native speaking language, I would very appreciate if you can drop me a line to point out any error (e.g. grammer, typo etc.) whenever you see it here.