Bioinformatics in the Classroom

Genes in Databases - Exercise 4

    Exercise 4 - Search For Information About Genes, Proteins, and Diseases Using Sequences

      Databases are rich sources to find all types of gen-related information: DNA sequences, protein sequences, gene regulation data, disease data, as well as data on genetic variation, gene homology and gene similarity, etc.. Search databases for in-depth information about the genes of any of these sequences.

        You may want to start your search at NCBI, and then, using some of your results as search phrases, extent it to any of these sites:

        • Entrez, the NCBI 'hub', which links sequence databases (GenBank, SwissProt) with publications (Pubmed) and information on diseases (Genes and Disease);
        • Genes and Disease;
        • OMIM, Online Mendelian Inheritance in Man;
        • Ensembl, genome browser of the European Molecular Biology Laboratories;
        • UCSC Genome Browser;
        • SRS (Sequence Retrieval System);
        • GeneCards, database on human genes and phenotypes;
        • SwissProt, Protein Database;
        • Celera, the company which contributed to the draft of the human genome;
        • Google, search engine.

        In your search try to find answers to these questions:
        • What characteristics does the gene have? (Length, exons, introns, splice sites, promotor, etc.)?
        • Examine the nucleotide and protein sequences; can you identify start and stop codons, splice sites?
        • Find the location in the genome. Can you locate the gene on a chromosome?
        • Which genes are located nearby?
        • Can you identify any 'unusual' features (alternative splicing, genes-in-genes, genes-ad-genes, etc.).
        • Can you identify any variations in the gene? (SNPs, insertions, etc.)
        • Can you find any pseudogenes of the gene?
        • Can you identify similar genes in the same organism? In other organisms? Are these orthologs or paralogs?
        • Can you find any references to the experiments that lead to the identification of the gene?
        • Can you find any information about the biology of the gene?
        • Can you identify any gene product? If it is a protein, what kind of a protein is it? Are there other proteins with similar functions?
        • Can you identify PCR primers that could be used as markers for the gene?
        • What does the gene look like on a cytogenetic map?
        • Can you find places that list mainly disease-related genes? In humans? In other organisms?

Go on to Exercise 5 - Retrieving information about Genes and Diseases, Keyword Searches

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