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, 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 222 (as of 15/02/05) completely sequenced bacterial genomes 21 Archaea 201 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.