Instructions for Performing BLASTN Analysis
are now going to perform a BLAST search using the wild-type sequence(s) that you
retrieved at the beginning of the semester. If you have more than one sequence,
you will need to perform these steps for each of the sequences.
Copy and paste the sequence that you want to analyze.
Go to the BLAST link:
will do a standard nucleotide-nucleotide search (BLASTN). Paste the fly gene
sequence that you copied from your Word file into the box and be sure that you are
searching the "Others (nr etc.)"
database (default is set at human for some reason). A new line will appear
labelled "Organism". Enter "Drosophila" in the text box and check the box
This will remove all Drosophila sequences from your results and make analysis more convenient.
You will also need to select “More dissimilar sequences (discontiguous megablast)” in the “Program Selection” box.
Finally, click the word "BLAST".
The first screen that loads is just to let you know that you will be waiting for the program to finish the search.
(Sometimes the wait
can be several minutes so be patient).
The final reload page will contain the results of the BLASTN search. The page has 3 sections. The first section is a graphic showing locations of similarity between your sequence (the query sequence) and some of the similar sequences that were identified by the program. The second section is a table of sequences similar to your query sequence with numerical scores (E values). The third section shows the actual alignments of your query sequence with each of the matching sequences.
The default number of hits is 100 (usually), so if this isn't enough to find what you are looking for, go back to the BLASTN page with the box, redo everything, and click on "Algorithm Parameters" at the bottom of the page before hitting the Blast button. This allows you to change the number of alignments that you will receive so that you have a chance of finding the correct hit.