Sequence tools
Type - for a gap. The table below lines the columns up.
A gap of n residues costs gap open + (n − 1) × gap extend.
Or click a column: the nearer end of the stretch moves to it.
With A=0, C=1, G=2 and T=3 a word is a number written in base 4 — two bits a base. There are 4k possible words and 4k shelves, so every word has a shelf of its own, and no two words ever collide.
Every word of every subject is filed on the shelf its number names, with the subject it
came from and the position it sits at. Classic BLAST does this the other way round — it
builds the table from the query and streams the database past it — but a database index
is real too: it is what makembindex builds for indexed megablast. The
lookup is the same either way.