Attempt at running a BLAST search
Jenae Skelton
10-23-12
First, I ran a nucleotide BLAST search for our entire sequence. Under the “Database” drop down
menu I selected the “Reference genome sequences (refseq_genome)” option instead of the human or
mouse genome. Under “Organism” I selected “maize (taxid:4577)” and “maize (taxid:381124)” since
we are going under the assumption that this is a sequence from the maize genome. Then I clicked the
BLAST button to start the search.
This query produced only one result: Zea mays chloroplast, complete genome.
Then I ran a protein BLAST search for our entire sequence. I used the “Non-redundant protein
sequences (nr)” database and the same organism categories as the previous search. This search failed to
run and only gave an error message that stated “Message ID#24 Error: Failed to read the Blast query:
Nucleotide FASTA provided for protein sequence.” I realized after the fact that I should have done a
BLASTx search since I was looking for proteins using a nucleotide sequence.
So I went back to the original BLASTn results and opened the accession number in a new
window. I clicked on the “Run BLAST” on the side bar under “Analyze This Sequence.” This produced
a list of 170 Blast hits.
This is what I have so far. I have no idea if I even did any of this correctly. I have no idea what the next
step should be. I don’t know if this is helpful to any of you, but I wanted to play around with the BLAST
search to see if I could even run it. Since this is possibly the chloroplast genome, do we need to list all
the proteins encoded in it? I don’t know where we should go from here, or if this is even the right
analysis and results we should have received.