How to use rpsblast+

[angeloulivieri]

Hi all,
I've problems in the understanding of how to use rpsblast+ by command line.
I can't found a good explanation anywhere! And i've been searching the web for a lot of hours.
Is anyone experienced in its use and can explain me in basic steps what I have to do?
In example:
1. download the CDD db from....
2. install it in ... (folder)
3. run rpsblast+ or some other command to manage the CDD...

Thank you very much

[angeloulivieri]

Ok. I was hoping in someone help.... now I discovered something doing a lot of googlesearch and trying.

If you want to run rpsblast+ by terminal you have to download a CDD database. You could find something at:

ftp://ftp.ncbi.nih.gov/blast/db/

The one called File:cdd_delta.tar.gz is good for the purpose.

Then upload the file on your system..

Now I'm trying doing a rpsblast+ on a file with 100 fasta sequences with this command:

rpsblast+ -query longTestSeq.fasta -db CDD/cdd_delta -out outRpsblast+


but I received:

"Database: cdd_delta.v3.07
24,198 sequences; 5,567,938 total letters

Query= comp173253_c0_seq1
Length=1717

***** No hits found *****"

I don't know if there's something wrong or I've done all good and this is the results..

[angeloulivieri]

No one has never used rpsblast+????
I'm searching on manuals, ncbi website and other infinite googleing...

[Votinhkiem90]

hi everyone.
I have a same problem, I have downloaded CDD database on NCBI and install ncbi-blast+. but when i run rpsblast have an error.
"BLAST Database error: Could not find volume or alias file (./home/lamnguyen/bin/ncbi-blast-2.2.29+/CDD/Cdd) referenced in alias file (/home/lamnguyen/bin/ncbi-blast-2.2.29+/bin/mycdd)"

mycdd has cread by http://www.ncbi.nlm.nih.gov/Structur....shtml#RPSBFtp

What should I do????:

[jocke_tuffing]

Hi!

I get this error message (that i don't get using another database in the same way):

[rpsblast 2.2.26] FATAL ERROR: Cannot map RPS BLAST profile file

Does anyone know how to solve this?

Thanks in advance!

/Olov

[jocke_tuffing]

Hi!

I get this error message (that i don't get using another database in the same way):

[rpsblast 2.2.26] FATAL ERROR: Cannot map RPS BLAST profile file

Does anyone know how to solve this?

Thanks in advance!

/Olov

Never mind. Switching to a more recent version of blast+ did it!