A master student from Brazil contacted me via email with questions how to run RPS-BLAST+ and cdd2cog.pl correctly. I'm copying the correspondence in here in case it is useful for someone else:
Hi, I am a master student of genetics at the Universidade Federal de Minas Gerais, Brasil. I was reading the cdd2goc description at
https://github.com/aleimba/bac-genomics-scripts/tree/master/cdd2cog#rps-blast
In the line referring to the use of RPS-Blast :
rpsblast -query protein.fasta -db Cog -out rps-blast.out -evalue 1e-2 -outfmt 6
I am confuse about the cog, which I highlighted. Is this another database we must download? If so, where could I find it, and to perform a search for protein sequences of a draft bacterial genome I assembled, how database should I get? Thank you in advance.
A master student from Brazil contacted me via email with questions how to run RPS-BLAST+ and
cdd2cog.plcorrectly. I'm copying the correspondence in here in case it is useful for someone else:Hi, I am a master student of genetics at the Universidade Federal de Minas Gerais, Brasil. I was reading the cdd2goc description at
https://github.com/aleimba/bac-genomics-scripts/tree/master/cdd2cog#rps-blast
In the line referring to the use of RPS-Blast :
rpsblast -query protein.fasta -db Cog -out rps-blast.out -evalue 1e-2 -outfmt 6
I am confuse about the cog, which I highlighted. Is this another database we must download? If so, where could I find it, and to perform a search for protein sequences of a draft bacterial genome I assembled, how database should I get? Thank you in advance.