MathBench > Probability

BLAST and (Im)probability

BLAST: Do try this at home!

So, for 165-nucleotide sequences, there are almost 1090 theoretical sequences for every actual archived (human genome) sequence. That's an awful lot of theoretical sequences that just aren't used (or at least haven't been found) in the human genome!

Another way of saying the same thing is this:

The chances of typing a RANDOM 165-nucleotide sequence into BLAST and getting a hit is 1 divided by 10 90 , or vanishingly small.

Using BLAST is almost as easy as searching in Google, just a bit slower. Yes, you can try this at home. First, tell the applet below to make a random sequence of whatever length you desire. (The applet will also tell you how many other similar-length sequences are possible). Then you can paste this sequence into BLAST to determine if it is a part of the human genome...

Number of bases:

Theoretical number of sequences:

Go to http://www.ncbi.nlm.nih.gov/blast/ , look for the heading "Basic BLAST", and under that heading, click on "nucleotide blast" (the first option). Paste in this sequence:

Make sure that "Human Genome" is selected in the Database box, then hit the big blue button labelled "BLAST" (it's at the bottom of the page). Usually the results take 10 seconds to a minute to load.

That's it -- just 5 clicks -- give it a try.

 

 

 

If you use a small number of bases (like 30), you'll probably get a long list of places where that PART of that nucleotide sequence has been found in the human genome. Looking at the "query coverage" will tell you how much of the sequence was found, and the bars near the top will tell you which part of the sequence was found.

Last time I tried it, I matched part of an olfactory receptor (among other things).

If you use a large number of bases (like 165), I'll bet you my Nancy Drew secret encoder ring that your report includes the words"No significant similarity found". That means blast can't find anything like what you're looking for.

Unless or until 1090 students try this, I'll most likely be keeping my ring!!