BIO306 Genetics: Lab BLAST Assignment (35 pts)

You have already obtained the DNA sequence that encodes the normal (“wild type”) version of the mutant gene (or genes) you are studying.  There are several predictions that can be made using this information.  The simplest is to predict the amino acids that are encoded by the sequence.  Analysis of the amino acid sequence of a protein can yield information about the possible functions and structures found in the protein. 

Another form of analysis is to compare the DNA sequence to other known sequences.  This can indicate how conserved a gene may be between different species.  Often, if we do not know the function of our gene, we can use the comparison of our DNA sequence with those previously described from other species to predict a similar gene whose function may be known, or at least more easily discovered.

In this experiment you will use your gene’s DNA sequence to do a BLASTN (BLAST, basic local alignment search tool, N, nucleotide) search of the Genbank database.  The list of results will consist of sequences from other non-Drosophila organisms. 

The output of the BLASTN search is a table of sequences and scores.  We will only focus on two columns of information from this table.  In the second column of the table, the name of the DNA sequence is listed as entered by the researchers who submitted the sequence. Further to the right is a column labeled “E value”.  The E value is a score that predicts the likelihood that your sequence and the sequence in the table aligned by random chance. 

Click here for instructions on how to perform the BLASTN search.

Click here for an example of a search with an analysis of the data.

Click here to download the questions that you must answer for the assignment.

Click here to access the papers needed to determine the wild-type function of your fly genes.