DAY 1c: Accessing Completed Genomes
1.
UCSC Genome Bioinformatics
2.
Ensembl
3.
NCBI Genomic Biology
3 major resources

Each of the 3 sites have strong points and weaknesses

UCSC - v. good graphics but only a few organisms.

Ensembl – not as user friendly as UCSC but more genomes & more
information.

NCBI – most genomes accessible here but poor graphics.
UCSC Genome Bioinformatics

Access the latest assembly of the human, chimp, cow, dog, mouse, rat,
opossum, chicken, X.tropicalis, zebrafish, tetradon, fugu, C.elegans,
C.briggsae, C.intestinalis, A.mellifera, A.gambiae, a number of
Drosophilae genomes, S.cerevisiae and the SARS genomes.

two major ways to do so:
 BLAT Search
 Genome Browser

BLAT search - find sequences of 95% and greater similarity of length
40 bases or more on the genome.

Ensembl is a joint project
between EMBL - EBI and the
Sanger Institute to develop a
software system which
produces and maintains
automatic annotation on
eukaryotic genomes.
NCBI Genomic Biology

Good starting point for accessing the human, mouse, Rat, Zebrafish,
Drosophila, Malaria, Plant, microbial and viral genomes.

Almost all genomic information is available through this site.

Human, Mouse, Rat, Zebrafish and Drosophila genomes can all be
accessed through Entrez Gene.
Plant Genomes Central

Resources for:
 Arabidopsis thaliana (thale cress)
 Gossypium (cotton)
 Hordeum vulgare (barley)
 Lycopersicon esculentum (tomato)
 Medicago truncatula (barrel medic)
 Oryza sativa (rice)
 Solanum tuberosum (potato)
 Triticum aestivum (bread wheat)
 Zea mays (corn)
Malaria

This resource provides data and information relevant to malaria
genetics and genomics.

The complete genomic sequence of the malaria parasite Plasmodium
falciparum and one of its major vectors Anopheles gambiae now
available.
Microbial Genomes

This resource provides links to the 279 (as of 07/11/05) completely
sequenced bacterial genomes

24 Archaea

255 eubacteria.
Retroviruses

Taxa-specific pages for HIV-1, HIV-2, SIV, HTLV, STLV.

Genotyping tool - uses the BLAST algorithm to identify the genotype
of a query sequence

Alignment tool - global alignment of multiple sequences

HIV-1 automatic sequence annotation - generates a report in GenBank
format for one or more query sequences

Genome maps - graphical representation of 50 retrovirus complete
genomes
A Few Other NCBI Resources

Unigene

Genes & disease

OMIM
Unigene

Experimental system for automatically partitioning GenBank
sequences into a non-redundant set of gene-oriented clusters.

Each UniGene cluster contains sequences that represent a unique gene,
as well as related information such as the tissue types in which the
gene has been expressed and map location.

Expressed sequence tag (EST) sequences have been included.
Genes & Disease

Information on diseases caused by mutation of a gene.

Classifies syndromes, diseases and conditions by sort:
– Cancer
– Immune system
– Muscle and bone
– Signals
– Transporters
– Nervous system
– etc.
Online Mendelian Inheritance in Man
(OMIM)

Catalogue of human genes and genetic disorders.

Contains textual information, pictures, and reference information.