Material linked from bioinformatics course


The blue arrows tell you where to click...

Step 1. Find BLAST. It is part of the MRS bioinformatics suite. And MRS can be found in the 'Pointers' window.

After activating BLAST, first cut-n-paste 'My beautiful sequence' in the sequence box (don't forget the >  sign up front; its a must). Second, choose the database in which you want BLAST to search for you; this must, of course, be the PDB because we want to find a structure file. Third, don't forget to click on 'Run Blast' because that will make the program work much faster...

After a second or so, BLAST is done. Now click on line that holds your results (you most likely will have only one line), and you get the next picture.

You see a series of 'hits'. Each hit indicates a PDB file (or just one protein chain in a PDB file if that PDB file holds more than one protein). The first hit is 1bqb.A; that is the chain labeled A in the PDB file 1BQB. Click on the bar to expand the results of the hit, and in the expanded results, click on the new bar(s) again. This should give you the next figure; your BLAST result.

The alignment made by BLAST. Feel free to ask the assistants what all things mean, but this is not exam-material...
The only thing that is important is the percentage identity. Look it up.