Exercise 1: Databases for the Storage and “Mining” of Genome/Gene/Protein Sequences

1. Finding Databases.
a. What major databases are available online that contain DNA and protein sequences?
b. Which database contains entire genomes?
c. Using online resources make sure you understand the meaning of the following terms.
i. BLAST
ii. Taxonomy
iii. gene ontology
iv. phylogenetic trees
v. multiple sequence alignment
d. Once you have defined these terms, find resources on the Internet which enable you to
study them. Get the URL.

2. NCBI Databases.
Explore the available databases of NCBI. Which database/s would be preferred if you are
looking for:
a. records of protein structures
b. human genes and genetic disorders
c. nucleic acid sequences of various species
d. viral genomes
e. transcript sequences, cDNA clones, protein similarities from the same gene locus
f. genes which are completely sequenced
g. phylogenetic lineages
h. DNA sequence chromatograms
i. macromolecular 3D structures
j. curated genomic DNA, RNA and protein sequences

3. J. Craig Venter Institute formerly TIGR (The Institute for Genomic Research) Exercise.
Open the site (http://www.jcvi.org). Find the Maize CellGenomics Database.
a. How many genes are reported in the db?
b. What is the public gene ID of PIP2-1 (AQUAPORIN)
c. How many variants are there for the gene and in which chromosome number is it
found?
d. Explore the UniProt identifier of the gene. What is the Taxonomic identifier?
e. How many amino acids are there for the protein? Copy the sequence (FASTA).
f. What literature was cited for the function, subunit and interaction with PIP1-2?

4. NCBI Entrez Exercise

a. Find which chromosome the gene KRT18 is located in the human genome.
b. List three organisms other than human which also have the KRT18 gene.
c. What protein is encoded by the KRT18 gene (describe)? What is the length of the
protein that is encoded by human KRT18 gene?
d. Copy the amino acid sequence of the human KRT18 nucleotide sequence and
amino acid sequence (FASTA format).