Introductory Exercise

Part: One

Q1: Use Google to search the web for bioinformatics institutes, centers, organizations, and other web sites that provide useful databases or bioinformatics tools. Provide 1 example with URL and indicate one important aspect of the web site that could be useful during this course or to your own research.

Q2: Use Google to search the web for a program to translate DNA into the encoded amino acid sequences.  List one possible web site with URL and indicate the organization responsible for this site.

Q3:Use Google to search for a website containing the Rat Genome project.  List one web site with URL and indicate which organization developed this site.
 
Q4: Identify a link in the BIR website for aligning two sequences.  List the web site with URL.
 
Q5: Identify an internet site which provides the BLAST search program, give URL.

Q6: Find a site listing information and sequence regarding the pGEM-3z plasmid (hint use keywords: pGEM-3z, plasmid, sequence), give URL of sequence listing and indicate size of the plasmid in base pairs (bp).

Part: Two

Go to the ENTREZ home page.  Answer the following questions using the keyword “oncostatin” to query the “Nucleotide”, “Protein”, “Structure”, “Entrez Gene”, and “OMIM” databases.
“Nucleotide” –

1. What is the accession number for the reference sequence (refseq) of human oncostatin M mRNA (Not the receptor!!)?(1 pt) 
2. Which sequences were the reference sequence derived from? (2 pt) 
3. Where does the protein coding sequence start and stop in the mRNA? (6 pt)
4. Indicate the chromosomal location of the human oncostatin M gene map? (2 pt)

“Protein” –

5. What is the accession number for the reference sequence (refseq) of the human oncostatin M precursor? (1 pt)
6. Does oncostatin M have a signal peptide?  If so, where is located?   What is a signal peptide?  (4 pt)
7. What is the size of the mature peptide after cleavage of the signal peptide?  (6 pt)
8. Link to the accession number:    AK155637 for the mouse oncostatin M mRNA sequence (Nucleotide database!).  Can you identify the signal peptide in the mouse Oncostatin M protein? Explain.

“Structure” –

9. Has a structure been determined for OSM?  If so what is the accession number? (4 pt)

“Entrez Gene” -

10. How many exons are present in the OSM gene?  (2 pt)
11. Is OSM part of a gene family?  (2 pts)
12. What is one  function of oncostatin M?  (4 pt)

“OMIM” –

13. What is the molecular weight of human oncostatin protein? (2 pt)
14. When was the OMIM record last updated?  (1 pt)
15. What is the accepted gene symbol for oncostatin M?  (2 pt)
16. What gene maps close to the human oncostatin M gene?  (4 pt)

EXTRA CREDIT

17. Identify the direction of transcription of the human oncostatin M gene compared to the closely mapping gene you identified in 15?   Are they in the same direction of transcription?   How did you determine this?  (6 pt)
18. Which exon encodes the signal peptide? (6 pt)
19. Is the RefSeq information about the size of the mature oncostatin M protein correct?  Explain.

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