Entering edit mode
5.7 years ago
enriqp02
▴
30
Hello guys!
I've been involved in a new project, where I'm going to analyze proteins from different soils. However, I have not found any consortium where all the proteins studied are together, as for example in the human microbiota.
Could anyone tell me which database could be used? I have thought about NCBI nr, but the search would be very long computationally
What do you mean by this? Are you sure "tedious" is the correct word here?
Hahaha. Maybe yes or maybe not. Depend of the context. I said tedious because the search will take days or weeks... so it will be very boring haha. Probably I translated it directly from Spanish, where that phrase would have a better meaning ahaha.
Anyway, I just wanted to say that this process will take a lot of computational time
If you want meaningful annotations, stick to SWISSPROT. NR isn't curated.
I've not used it previously, but this tool is supposedly much faster than NCBI's BLAST.
https://github.com/bbuchfink/diamond
Thanks for your reply.
Anyway I'm going to use Mascot or Sequest search engines to looking for matches. I just want to know what is the best database to do this.
Nobody with experience in this?
Hi enriqp02,
I have moved your response to a comment as answer field is reserved for answers to the original question.