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?
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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?
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Arthur Goldsipe
on 6 Nov 2014
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
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