Database Search

The goal of this section is to learn how to retrieve information according to several criteria from biological databases.

1. Retrieve the following list of protein sequences from the SWISS-PROT database
   http://www.uniprot.org/:
   1. $\lambda$-repressor.
   2. human MAP kinase inhibitor.
   3. human catalase.
   4. synechocystis cytochrome P450.
   5. coli DNA polymerase.
   6. HIV CCR5 receptor.
   7. Cholera dehydrogenase.
   Record your findings and study the annotations.
2. Use the NCBI Entrez database http://www.ncbi.nlm.nih.gov/ for the following searches. (Click link ``GenBank'' followed by link ``Search GenBank'' on the left of the page to come to the advanced search options page).
   1. Search for human kinase protein sequences that have been modified or added to GenBank within the last 30 days. (Hint: Choose ``Protein'' database from the pull-down-menu; enter ``human[Organism] AND kinase'' into the text-field; use link ``Limits'' to restrict results).
   2. Search for mouse fas antigen DNA sequences with annotated exons or introns. (Hint: Choose "Nucleotide" database from the pull-down-menu; enter ``mouse[Organism] AND fas AND (exons OR introns)'' into the text-field.)
   3. Study ``Help'' -> ``Writing Advanced Search Statements'' to learn how to design search strategies for the following queries. (Choose the appropriate database yourself)
      1. Find gene sequences for formate dehydrogenase from Methanobacterium.
      2. Find gene sequences for DNA binding proteins in Methanobacterium.
      3. Find all human nucleotide sequences with D-loop annotations.
      4. Find protein sequences of maltoporin in Gram-negative bacteria. (Hint: Gram-positive bacteria belong to Firmicutes).
      5. Find protein structures related to Rhizobium nodulation.
      6. Find review papers related to biofuels by Keasling.
      7. Find the number of exons and introns in Arabidopsis phytochromeA (phyA).
      8. Find two upstream neighboring genes for the hypoxanthine phosphoribosyl transferase (HPRT) gene in E. coli K12 genome.