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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

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slide1

Web site:

http://bioinfo.weizmann.ac.il/ws

Mailing list:

http://bioinfo.weizmann.ac.il/announce

Contact:

[email protected]

slide2

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

slide3

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

Genomic Databases:from primary DNA sequenceto gene function

Vered Chalifa-Caspi

Bioinformatics and Biological Computing Unit

Biological Services Department

Weizmann Institute of Science

slide10

http://dapsas.weizmann.ac.il

http://bioinfo.weizmann.ac.il

slide11

Genomic Databases

  • Genomic Sequences
  • mRNA Sequences
  • Genome Viewers
  • Gene Databases
  • Genetic Variation
  • Gene Expression
  • Protein Databases
  • Protein Classification
  • Pathways
genomic sequences13
Genomic sequences
  • All sequences are archived in GenBank/EMBL/DDBJ
  • Genomic sequences:- unfinished clones.- finished clones.- clone contigs.- entire chromosomes.- entire genomes.
mrna sequences16
mRNA sequences
  • Full mRNA sequences
  • Expressed Sequence Tags (ESTs)
  • EST clusters
  • EST assemblies
  • Predicted genes
slide20

By integrating map and sequence information,

a whole-genome view can be constructed

Annotation

Gene A

Predicted

gene K

Gene B

slide21

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
University of Californiaat Santa Cruz

http://genome.cse.ucsc.edu/

slide38

dbSNP

A central repository for both single base nucleotide

subsitutions and short deletion and insertion polymorphisms.

slide42

Edgar et al. Nucleic Acids Research, 2002, Vol. 30, No. 1 207-210

http://nar.oupjournals.org/cgi/content/full/30/1/207/GKF066TB1

slide48

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.

slide52

Search for a GO term and view all gene products annotated to it.

  • Search for a gene product
  • and view all its associations.
slide59

http://www.genome.ad.jp/kegg/regulation.html

KEGG: Kyoto Encyclopedia of Genes and Genomes

slide62

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

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