Blast+ in RAVEN

[parsanayyara]

Hello,

I noticed that RAVEN uses BLAST+ to run getBlast() for reconstructions, I followed the BLAST+ installation as noted on the website and install it on the RAVEN folder, but everytime I tried running checkInstallation on RAVEN, it kept giving this error. Can anyone give suggestions on how to properly get Blast+ installed for RAVEN?

[mihai-sysbio]

Hi @parsanayyara! Could you specify what operating system and what version of Matlab you are using?

[parsanayyara]

MATLAB R2022b in 64-bit Windows

[mihai-sysbio]

The executables for BLAST+ (as packaged with RAVEN) haven't been updated in two years https://github.com/SysBioChalmers/RAVEN/tree/main/software/blast%2B. We are distributing these, so there is no need to install BLAST+ separately. For testing purposes, could I ask you to fetch an older release v2.7.12 and see how that one behaves?

[parsanayyara]

I will try and do that. On another note though, suppose I manage to get it RAVEN up and running, would it be possible to do a reconstruction only based on MetaCyc and can the draft reconstruction generated by RAVEN be exported into excel or is it already in COBRA-compatible SBML?

[mihai-sysbio]

Instead of risking to not be giving the fully accurate answers here, I'm pinging @edkerk.
In general, I wouldn't worry about the export. To my knowledge, the SBML is COBRA-compatible, and there is Excel export as well.

[edkerk]

Regarding your MetaCyc question, you can make a reconstruction based only on MetaCyc but I would not recommend this as MetaCyc-based reconstruction tend to contain many false positive hits. Instead, MetaCyc-based reconstruction is best used as complementary approach, where the reactions are checked and curated before added to another (draft) model.

Finally, RAVEN exports valid SBML L3V1 FBCv2 files, which are COBRA-compatible. I strongly discourage the use of Excel as intermediate file format. Excel can be great if you quickly want to look up some aspects of the model (and are a proficient Excel-user), but should not be used to make changes to the model.

[edkerk]

I cannot replicate the non-functioning BLASTP executable, you can perhaps run blastPlusTests to get more information.