Start MRS. The opening screen looks like this:
Click on BLAST in the left column to start the program. Below, you see an example containing the amino acid sequence of the first suspect. The first line should always start with a >, followed by the name of the protein (this is the so-called FastA format). Here we chose the name suspect1.
Go to the webpage that shows the list of unidentified proteins. The amino acid sequences of the 4 candidate proteins are written in the correct format for use in MRS.
Filter sequence (low complexity) box is
clearedRun BLAST (top right of the window)
You are now forwarded to the next screen, showing running while BLAST is busy. If many people are using BLAST simultaneously, this may take some time. Do not forget that you are working with a database containing hundreds of thousands of protein sequences.
When the search is completed, a table showing the results appears, which looks like the one given here
(the numbers may vary because of SwissProt updates) :
This output means that 89 hits have been found in the SwissProt database. In other words, 89 proteins have an amino acid sequence similar to suspect1. The number under e-Value
shows how good the best result is. If this number is small (which is
the case here, since it is 5.36 x 10-113), the result is reliable.
Note: If you want to look at the different suspects again, you can open previous results by clicking BLAST results in the left column.
Click on the line (it will turn blue) to get more details about the results. The following screen appears:
This screen gives you the so-called hitlist, the list of protein sequences found in the SwissProt database that are similar to suspect1. The protein at the top is the most similar to your query sequence, suspect1 (in fact, it is identical). The code of the sequence is casa1_bovin.
From left to right, every line shows the following output for each one of the hits:
Nr: The number of the result. Number 1 always shows the best hit, and so onID: This is the code of the protein sequence from the database. The first part of the code (casa1) is the name of the protein, the second part contains the (shortened) name of the organism, in this case bovine.Coverage: The coloured line shows which part of your query sequence (suspect1)
matches the database sequence (the grey background). On the first line, you can see that your
query sequence matches the casa1_bovin sequence over its
entire length.Description: a brief description of the database sequence matching your queryHsps, Bitscore, and E-value: Values calculated by BLAST to give you an idea about the reliability of the result. The best hit is always on top.
