Bioinformatics

1. GENOME resources

2. WHAT IS A GENOME?
 Organism’s whole hereditary information
 includes both the genes and the non-
coding sequences of the DNA
 complete DNA sequence of one set of
chromosomes.
 term was coined in 1920 by Hans Winkler

3. SOME GENOME DBs
 Human
 OMIM (Mendelian Inheritance in Man)
 GDB(Human Genome Data Base)
 TIGR database
 Genethon database

4. Cont,
 Plant
 USDA/ARS/National Agricultural Library Plant Genome Data
 (NAL) National Agricultural Library; Plant Genomes
 AAtDB browse An Arabidopsis thaliana genome database at NAL - query
 AAtDB at Harvard U. - Search
 Arabidopsis Expressed Sequence Tags (EST's)
 Arabidopsis Information Management System (AIMS)
 U. Minnesota Arabidopsis cDNA sequencing Project
 Alfagenes browse Alfalfa genome database at NAL query
 BeanRef
 BeanGenes browse Bean genome database at NAL query

5.  ChlamyDB browse Chlamydomonas database at NAL query
 CottonDB browse Gossypium sp. database at NAL query
 GrainGenes browse query
 MaizeDB browse Maize genome database at NAL query
 MaizeDB Maize Genome Database
 RiceGenes browse Rice genome database at NAL query
 Japan Rice Genome Research Program (RGP)
 SorghumDB browse Sorghum bicolor database at NAL query
 SoyBase browse Soybean genome database at NAL query
 TreeGenes browse Forest trees database at NAL query
 Mendel browse Plant-wide gene names database at NAL query

6.  Drosophila
 Drosophila database
 FlyDB
 Carthew Drosophila Lab
 Nagoshi Lab Home Page (Drosophila)
 FlyView - A Drosophila Image Database
 Other Insects
 National Insect Genetic Resources
 Sericultural Science, the University of Tokyo

7.  Fungal
 Mycology at Cornell
 Saccharomyces genomic database
 LISTA A Compilation of Sequences from Saccharomyces
 Yeast Protein Database (YPD)
 MycDB Mycobacterium Database
 MycDB browse at NAL query
 Candida albicans
 FGSC Fungal Genetics Stock Center
 Eschericia coli
 EcoCyc: Encyclopedia of E. coli Genes and Metabolism
 ECDC (E. coli Database Collection)
 Other Prokaryotes
 Normalized Gene Designation Database (NGDD)

11. Ensembl
 Contains all the human genome DNA
sequences currently available in the public
domain.
 Automated annotation: by using different
software tools, features are identified in the
DNA sequences:
 Genes (known or predicted)
 Single nucleotide polymorphisms (SNPs)
 Repeats
 Homologies
 Created and maintained by the EBI and the
Sanger Center (UK)
 www.ensembl.org

22.  http://www.bioscience.org/
 http://genome.ucsc.edu/
 www.genomesonline.org/
 http://www.ebi.ac.uk/ensembl/
 www.genomenewsnetwork.com