Transcript Genome and Bioinformatics

Web site:
http://bioinfo.weizmann.ac.il/ws
Mailing list:
http://bioinfo.weizmann.ac.il/announce
Contact:
[email protected]
Genomic Databases and Analysis Tools
09:00-09:45
Vered Chalifa-Caspi
Genomic Databases: from primary DNA sequence to gene function
09:45-11:00
Shifra Ben-Dor
States of the human and mouse genomes
11:00-11:15
Coffee Break
11:15-12:15
Nili Avidan
Web-based analysis and annotation tools
12:15-13:00
Marilyn Safran
GeneCards: a database of human genes, their products and their
involvement in diseases
13:00-14:00
Lunch Break
14:00-16:00
Hands-on at Ebner Computer Classroom
Genomic Databases:
from primary DNA sequence
to gene function
Vered Chalifa-Caspi
Bioinformatics and Biological Computing Unit
Biological Services Department
Weizmann Institute of Science
SNPs
Nucleotide
sequence
AAGTGC C AC TGC ATAAATGA C C ATGAGTGG GC AC C G GTAAGGGA GGGTGATGC TATC TGG TC TG AA
Genes
mRNA
Protein
primary
sequence
Protein 3D
structure
Protein
Function
Acts as a tumor suppressor in
many tumor types. induces grow th
arrest or apoptosis depending on the
physiological circumstances or cell
type, but both activities are
involved in tumor suppression.
Involved in the transport of
chloride ions. Defects in CFTR
are the cause of cystic f ibrosis.
It is the most common genetic disease
in the caucasian population, w ith a
prevalence of about 1 in 2000 live
births. cf , an autosomal recessive
disorder, is a common generalized
disorder of exocrine gland f unction
Starting Points
for Navigation
http://www.ncbi.nlm.nih.gov
http://www.ebi.ac.uk/
http://dapsas.weizmann.ac.il
http://bioinfo.weizmann.ac.il
Genomic Databases
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Genomic Sequences
mRNA Sequences
Genome Viewers
Gene Databases
Genetic Variation
Gene Expression
Protein Databases
Protein Classification
Pathways
Genomic Sequences
Genomic sequences
• All sequences are archived in
GenBank/EMBL/DDBJ
• Genomic sequences:
- unfinished clones.
- finished clones.
- clone contigs.
- entire chromosomes.
- entire genomes.
mRNA Sequences
mRNA sequences
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Full mRNA sequences
Expressed Sequence Tags (ESTs)
EST clusters
EST assemblies
• Predicted genes
Genomic, mRNA and EST sequences
Clones:
Genomic
mRNA
ESTs
Genome Viewers
By integrating map and sequence information,
a whole-genome view can be constructed
Annotation
Gene A
Predicted
gene K
Gene B
Resources for whole human genome
sequence assembly
1. Human Genome Project Working Draft at the
University of California at Santa Cruz
2. Ensembl
EMBL - EBI and the Sanger Institute
3. MapViewer at NCBI
University of California
at Santa Cruz
http://genome.cse.ucsc.edu/
Gene Databases
Genetic Variation
http://archive.uwcm.ac.uk/uwcm/mg/hgmd0.html
Search for BRCA1
BRCA1 - Nucleotide substitutions (missense / nonsense)
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http://www.geneclinics.org/
http://ariel.ucs.unimelb.edu.au:80/~cotton/glsdb.htm
http://www.ncbi.nlm.nih.gov/SNP/
dbSNP
A central repository for both single base nucleotide
subsitutions and short deletion and insertion polymorphisms.
http://hgvbase.cgb.ki.se/
Gene Expression
Edgar et al. Nucleic Acids Research, 2002, Vol. 30, No. 1 207-210
http://nar.oupjournals.org/cgi/content/full/30/1/207/GKF066TB1
http://www.ncbi.nlm.nih.gov/geo/
http://www.hugeindex.org
Protein Databases
http://www.expasy.ch/sprot/
http://www.ebi.ac.uk/interpro/
Integrated resource of Protein Families, Domains and Sites.
Unifies signature databases (PROSITE, PRINTS, ProDom, Pfam,
SMART, TIGRFAMs)
Useful for:
- Identifying distant relationships in novel sequences
- Predicting protein function and structure.
- Large-scale genome annotation.
Protein Classification
http://www.geneontology.org/
• Search for a GO term and view all
gene products annotated to it.
• Search for a gene product
and view all its associations.
Pathways
http://inn.weizmann.ac.il/units/dna_array/dna_array.html
http://www.genome.ad.jp/kegg/regulation.html
KEGG: Kyoto Encyclopedia of Genes and Genomes
Thank You!
Genomic Databases and Analysis Tools
09:00-09:45
Vered Chalifa-Caspi
Genomic Databases: from primary DNA sequence to gene function
09:45-11:00
Shifra Ben-Dor
States of the human and mouse genomes
11:00-11:15
Coffee Break