Genome Analysis
- Ms. Sheetal Gajarlawar.
What is a Genome?
• All of the genetic information, the entire genetic complement,
all of the hereditary material possessed by an organism.
• The term was adapted in 1920 by Hans Winkler, Professor of
Botany at the University of Hamburg, Germany.
• Humans and many other higher animals actually have two
genomes, which together make up the total genome:
– A chromosomal genome -- inside the nucleus of the cell in the
familiar form of chromosomes; and
– A mitochondrial genome -- outside the nucleus in the cytoplasm of
the cell, usually in the form of one round chromosome (the
mitochondrial chromosome).
• The total genetic content contained in a haploid set of
chromosomes in eukaryotes, in a single chromosome in
bacteria, or in the DNA or RNA of viruses
• The human genome is made up of approximately 35000
genes, or three billion chemical base pairs.
Genome Analysis
• A major application of bioinformatics is analysis of the full genomes
of organisms that have been sequenced starting in the late 1990s,
including over 100 microbial genomes, yeast (Saccharomyces
cerevisiae), nematode (Caenorhabditis elegans), plants
(Arabidopsis thaliana), fruit fly (Drosophila), the human genome, as
well as many organisms that are human pathogens.
• Many additional genome sequencing projects have been
completed and others are planned or under way.
• Genomic analysis are the techniques needed to determine and
compare the genetic sequence (e.g. DNA in the chromosomes and
mitochondria). This includes DNA sequencing, routine use of DNA
microarray technology for the analysis of gene expression profiles
at the mRNA level and improved informatic tools to organize and
analyze such data. At the same time, new developments in chip-
based analysis of samples and the emergence of models of gene
networks.
• Database Web address
• A. thaliana information resource TAIR http://www.arabidopsis.org/
• Caenorhabditis elegans (worm) database http://www.wormbase.org/
• Cold Spring Harbor Laboratory Genome Projects http://www.cshl.org/
• DOE Human Genome http://www.doegenomes.org/
• Drosophila genome project Berkeley http://www.fruitfly.org/
• Drosophila: Flybase, a genomic database http://flybase.bio.indiana.edu/
• E. coli genome project http://www.genome.wisc.edu/
• ENSEMBL e! genome browser (Sanger Inst., EMBL-EBI) http://www.ensembl.org/
• Genome list at NIH http://molbio.info.nih.gov/molbio/db.html
• Genome database in support of human genome project http://www.gdb.org
• Gramene—cereal grasseshttp://www.gramene.org
• Human Genome Browser (Golden Path, UCSC) http://genome.ucsc.edu/goldenPath/hgTracks.html
• Mouse (Mus musculus) genome informatics http://www.informatics.jax.org/
• National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/
• NIH Human Genome Res. Initiative NHGRI http://www.genome.gov/
• Parasite genome databases http://www.ebi.ac.uk/parasites/parasite-genome.html
• PIR Georgetown University genomes http://www-nbrf.georgetown.edu/pir/genome.html
• Prokaryotic genomes P. Bork laboratory http://www.bork.embl-heidelberg.de/Genome/
• Rice (Oryza sativa) genome project http://rgp.dna.affrc.go.jp/
• S. cerevisiae (budding yeast) database (SGD) http://genome-www.stanford.edu/Saccharomyces
/
• Stanford University genome resourceshttp://genome-www.stanford.edu/
• The Institute of Genomics Research (TIGR) http://www.tigr.org/
• The Sanger Institute http://www.sanger.ac.uk/
• U.S. Dept. of Energy Joint Genome Initiative http://www.jgi.doe.gov/
• Washington University Genome Center http://genome.wustl.edu/
• Whitehead and Broad Institutes for Biomedical Research http://www.broad.mit.edu/genome.html/
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