Formatdb has been deprecated by BLAST in favor makeblastdb, yet matlab 2014b still tries to use formatdb when using the blastformat.. is there any way around this?

Matlab does not include makeblastdb for blastformat, yet BLAST does not support the use of formatdb that Matlab still uses. Is there a way to fix this?

Answer 1

[Arthur Goldsipe]

Hi,

MATLAB doesn't actually ship with formatdb. blastformat required you to download formatdb, and the MATLAB function basically just runs this utility.

I think you can just download makeblastdb and call it, either from within MATLAB or within a command shell. If you want to call it from within MATLAB, you can use the system function. Maybe you can take a look at the definition of the blastformat function to get some ideas on how to do that.

-Arthur