Question: What are the "Coding", "Maximal" and "Two templates" options for megablast?
gravatar for Superbest
5.0 years ago by
United States
Superbest120 wrote:

"discontiguous megablast" on the NCBI website, as well as other implementations, appears to have a "Discontiguous Word Options" parameter set. These include a template length and template type; the latter can be:

  • Coding
  • Maximal
  • Two templates

What do these options do?

blast • 1.5k views
ADD COMMENTlink modified 5.0 years ago by Asaf5.6k • written 5.0 years ago by Superbest120
gravatar for Asaf
5.0 years ago by
Asaf5.6k wrote:

The way BLAST works is by first matching a word from the query and the database, this match is then expanded using dynamic programming. The word is usually 7-256 in length. When using discontiguous BLAST the word is 11-12 letters in a 25 letters long sequence. The way these letters that must match between the query and database are spread differently along the longer sequence. In coding the matching letters will be in the first two nucleotides of every triplet, in maximal they will be spread in a predefined pattern that should maximize the number of matches, two templates just try to match these two patterns.

In short discontiguous BLAST allows matches that don't have a 7 letters word that perfectly match between the two.
ADD COMMENTlink written 5.0 years ago by Asaf5.6k

So "coding" is good for actual ORFs, "maximal" is good for everything else, and "Two templates" just does both?

ADD REPLYlink written 5.0 years ago by Superbest120

Exactly, although if you're looking for ORFs you should probably use tblastx

ADD REPLYlink written 5.0 years ago by Asaf5.6k
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