Lab Exercise: Bioinformatics

Blast exercise

The gene DCC is deleted in colorectal cancer and is located on human chromosome 18q21.3. It encodes for a tumor suppressor protein. Expression of the gene is reduced significantly in most colorectal carcinomas. The protein sequence of human DCC has the Refseq accession number of NP_005206.

•Locate the Genbank record for this protein. Note the length of the amino acid sequence.

• Perform a BLASTP search using this protein as the query and Swiss-Prot as the target database. Limit the search to mammalian species only and use BLOSUM62 as the scoring matrix.

• The DCC protein from human is most closely related to the DCC protein from what other mammal?

• What percent identity do they share?

• What is their percent similarity?

• What is the length of the alignment? Were both proteins aligned along their entire length?

• Does the DCC protein contain any low-complexity regions that have been masked out by BLASTP? If so, where?

• Look at the results for protein with Swiss-Prot id of P97798.

• What percent identity does it share with the query?

• What is the alignment length? Is it a global or local alignment for the query and the target?

• Would you say this protein is homologous to the query?

• Look at the results for protein with Swiss-Prot id of O60469.

• What's the %id and length of the alignment? Can you assert homology?

• Is this a global or a local alignment with respect to the query? How about with respect to the target?

• Based on the BLASTP results, can any general observations be made regarding the putative function or cellular role of DCC?