Introduction to Bioinformatics - Biol 591

 

SCENARIO
Detecting a stealth anthrax toxin gene
The truth behind Blast

...but the protein sequence tells a different story
Now you are flabbergasted! How is it that searching for similar DNA sequences yields no significant similarity to lef but searching for protein sequences gives you perfect identity! Something must be real funny with this DNA sequence, so you compare it by hand with the corresponding DNA sequence from lef, getting the alignment shown here.
sample protein
...TATLGADLVDS...
...TATLGADLVDS...
toxin protein

... Perfect identity!

Things are not getting any clearer. The gene fragment is highly similar to lef, about 90% identical. That's consistent with the identity of the protein sequences, BUT THEN WHY DIDN'T BLAST FIND THE DNA SEQUENCE??? In desperation, you compare the two DNA sequences by pairwise Blast. Of course, you already know the answer -- you just did the same comparison by hand. You just want to see if Blast has gone crazy.

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