CLASS 2. Biological Database Search Exercise.

INSTRUCTIONS:

For each exercise, provide search query used and keep the answers brief. Email me the answers by Sunday 11:59PM AST at the latest.

Use "CLASS 2 EXERCISE" as a message subject, and type answers directly to email body (i.e., no document attachments please). Make sure that first line of your message is your NAME.
LINKS:

  1. Using PubMed, find out how many research articles did Russell Doolittle and Ford Doolittle co-author?

  2. What article corresponds to the first record ever made in PubMed database? How many related articles does it have? When was the most recent related article published? Is the original article associated with any DNA or protein data?

  3. When researchers discuss phenomenon of "horizontal gene transfer", some use "lateral gene transfer" as a synonym. How many research articles use "horizontal gene transfer" in their title or abstract? How many research articles use "lateral gene transfer" in their title or abstract? What query would you use to find the number of research articles that use either of the two terms? Do numbers from your last query add up to the results of the previous two queries? Why or why not?

  4. After hearing the Science magazine podcast interview with Dr. Tim White, you learned about new hominid fossil evidence published in this journal recently. How would you go about finding the corresponding research article? [podcast, not required to listen to answer the question]. Report PubMed ID (PMID) in your answer.

  5. How many REVIEW articles have word "BIOINFORMATICS" in their title?

  6. Using ISI's Web of Science database (choose the "Web of Science" tab at the top), search for articles that cite work of Elizabeth H. Blackburn, 2009 Nobel Prize Winner in Physiology and Medicine. Which was the most cited article? How often was it cited? Is it the article she received a Nobel Prize for ("for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase")? When was the most recent citation?

  7. Find complete genome record(s) corresponding to Escherichia coli strain K12 chromosome(s). How many did you find? Why? Report accession number(s). [Use Nucleotide database with Limits and Preview/Index for this exercise]

  8. How many nucleotide sequences from influenza A virus H1N1 subtype is currently available in GenBank? [Hint: use taxonomy database as a starting point]

  9. How many genomes are completed within bacterial order Thermotogales?

  10. Examine revision history for sequence with accession number "NM_024744". What is the current version number? Compare current version with some of the previous versions. What kinds of changes had occur to this record?