Digging In: Hands-on Experience with NCBI's Molecular Databases (Exercises)

Exercises

	GENE STORY #1: HUMAN MLH1 GENE IMPLICATED IN COLON CANCER

A1	Retrieve concise list of sequence records for a topic: colon cancer	Question	Answer

A2	Retrieve associated literature and protein records	Question	Answer

A3	Identify conserved domains within the protein	Question	Answer

A4	Identify similar proteins	Question	Answer

A5	Identify known mutations within the gene or protein	Question	Answer

A6	Find a resolved three-dimensional structure for the protein, or in its absence, identify structures with homologous sequence	Question	Answer

A7	View genomic context and download the sequence region	Question	Answer

A8	Find a locus-specific record that summarizes a wide range of information about the MLH1 gene in a single record	Question	Answer

	GENE STORY #2: HUMAN PER (PERIOD) GENE, IMPORTANT IN CIRCADIAN RHYTHMS

B1	Find concise summary of genes pertaining to a specific area of research: circadian rhythms	Question	Answer

B2	Identify the gene involved in a specific sleep disorder	Question	Answer

B3	Compare a gene sequence from normal versus diseased patients	Question	Answer

B4	View a structure to examine the significance of a conserved domain	Question	Answer

B5	Find the location of the PER2 gene, and download the sequence for the gene plus the promoter region	Question	Answer

B6	Gather Sequence Data and Related Information on a Particular Genetic Locus	Question	Answer

	USER QUESTION GRAB BAG

C1	Find putative identify of a sequence generated by a lab	Question	Answer

C2	BLAST search with short query sequence	Question	Answer

C3	Retrieve nucleotide sequences from a specific organism, gene, and molecule type, and exclude a certain subset of sequences (ESTs) from the results	Question	Answer

C4	Retrieve all protein sequences for a specific taxonomic node	Question	Answer

C5	View summary information for a protein structure, and view its corresponding 3-D image	Question	Answer

C6	Find the location of a gene in the human genome and the location of the homologous gene in the mouse	Question	Answer

C7	Find the official symbol and alternate symbols that have been used for a gene	Question	Answer

C8	Download the complete genome sequence for a bacterium of interest	Question	Answer

C9	Find clinical information about a genetic disease and identify labs that offer genetic testing for that disease	Question	Answer

C10	Identify the genes that exist in a specific cytogenetic band	Question	Answer

C11	Identify the STSs that exist in a specific gene	Question	Answer