Nucleotide-Nucleotide BLAST (blastn)

Now that we have explored the program and database options, let's do a basic blastn search with the Jurassic Park sequence that you have copied/pasted into memory. If you haven't already copied the query sequence into memory, please do it now.

One more note before we do the search...

The nucleotide BLAST page provides a selection of three programs that vary in their sensitivity and speed: megablast (default), discontiguous megablast, and blastn.

For our sample search, use the traditional blastn program.

Footnote, for your future reference. Some of the differences between the algorithms are highlighted below.

Megablast	Retrieves highly similar sequences and is very fast. It efficiently find long alignments between very similar sequences -- it is intended for comparing a query to closely related sequences and works best if the target percent identity is 95% or more. (word size* is 28 base pairs). learn more...
Discontiguous megablast	Retrieves more dissimilar sequences than megablast, but is more sensitive than blastn. It uses an initial seed that ignores some bases (allowing mismatches) and is intended for cross-species comparisons -- the third base wobbling is taken into consideration by focusing on finding matches at the first and second codon positions while ignoring the mismatches in the third position. (word size* can be set only at 11 or 12 base pairs.) learn more...
Blastn	Retrieves somewhat similar sequences, so can find more distantly related sequences, but is slower than megablast and discontiguous megablast. (default word size* can range from 7 base pairs to 11 (default) base pairs) learn more...

* Word Size is discussed later in the module in the slide on how did BLAST work. It is mentioned here only so this slide can serve as a useful reference after the course.