You have determined the base sequence for a gene from Felis catus (domestic cat) that you believe may be involved in feline leukemia. A BLASTn search results in nucleotide sequence matches from viruses, not mammals, although the similarity is low

Question

What other bioinformatic tools or techniques could you use to investigate the function of this gene? Why would these tools or techniques be more convincing than a BLASTn search? Hypothesize why you think this result might be correct or incorrect.
What will be an ideal response?

Answer 1

Answer: Another bioinformatics technique that could be used is a tblastx search, which takes the nucleotide sequence, translates all three reading frames into amino acid sequences, and searches for similar amino acid sequences in a protein database. This type of search may reveal whether there are conserved amino acid sequences between the new (query) protein and the matches in the protein database. Matching protein sequences can be more meaningful because nucleotide sequences are subject to drift, especially in the third (wobble) position of the codon. Protein databases may also contain information on protein domains and features that may shed more light on the possible function of the putative protein (Note: This part of the question could be changed to ask the student to think about any number of other techniques that were emphasized in class rather than a bioinformatics tool.)

It is possible that the result is correct in identifying viral sequences as the best match in the database. Cancer can be caused by viruses, in particular retroviruses that insert their genome in the host cell genome. Also, there are many retroviral-related sequences in mammalian genomes such as LINES and SINES. Further laboratory experiments, such as isolation of the protein, will need to be done to determine the properties, expression, and function of the putative protein. (Note: The instructor should judge this part of the question based on what has been presented in class over the course of the semester. The sophistication of the answers could vary widely depending on what has been previously covered in class. For instance, if cancer and viruses have not been discussed, the students may conclude that the viral sequences may be from viral contamination.)