Bioinformatics

1. The following paper appeared in PubMed in 2011: Cathepsin E (EC 3.4.23.34) – a review. Find all human (homo sapiens) cathepsin E proteins in the NCBI protein database
a. What class of enzyme does Cathepsin E belong to?
b. Find all human (homo sapiens) cathepsin E proteins in the NCBI protein database How many records?
c. Write the accession numbers of the Cathepsin E containing 396 amino acids. Accession:

2. Find the nucleotide record with the accession number NM_005368.3.
a. How is this sequence described in the definition field?
b. How many exons are annotated in the Features?
c. Look at the revision history. What is the latest date did the sequence change?

3. Find the human NOD2 gene in the Gene database at NCBI.
a. According to the summary, mutations in this gene are associated with what diseases?
b. Open the Blau syndrome record. What is the inheritance pattern of this disorder?
c. Get the CARD15 gene. Do a little searching of the internet. Are CARD15 and NOD2 separate genes or the same gene?

4. Go to the MeSH database and type in serine protease (without quotes). The first hit is the preferred term. Open that record in order to search PubMed. To search PubMed, click Add to search builder. Then click Search PubMed.

a. How many records?
b. Narrow the search in part a to find all articles on the topic whose authors include someone named Eschenberg (sp?). You are not sure of the spelling of Dr. Eschenbergs name. Specifically, you do not know whether it is spelled berg or burg. How many records?
c. Find the most recent paper in which S. Eschenburg is a first author. Pull up the abstract. Name the title of the paper and inhibitor of subtilisin DY.
Hint: For spelling, you can use the OR Boolean operator or you can truncate the name with an asterisk

5. Search for human protein records with CFTR in the protein field and then use UniProtKB/Swiss-Prot database for your search.
Open the record with the accession number Accession: P13569.3. What is the prevalence of cystic fibrosis in the Caucasian population (hint CTRL-F is a Find on Page feature of most browsers)?
Click ‘Identical Proteins’ to get sequences related to this protein. The first non-human match should be to a synthetic construct. Open that Protein record. What vector was this cDNA cloned?
Click ‘GenPept’ drop down and then Revision History. When was this record first seen and when was it first modified (the date after first entry)?

Last Completed Projects