Incomplete Blast Database In Ubuntu

Question

[rehma.ar]

hello all, i am trying to do local blast using this command

 blastall -p blastn -n T -i query.fasta -d nt.12 -o /blast.out

i am doing a "blastn" , "-n T" shows i want to megablast. i have downloaded database "nt.12' from NCBI website.(assuming that its latest). but when i run this command i get a different result than the result i get when i do this blast at NCBI with default settings.

i noticed that blast version on my computer is "BLASTN 2.2.21 [Jun-14-2009]" but on the NCBI site its "BLASTN 2.2.27" so i think the problem lies with version of blast.

can anyone guide me to update my blast version to "BLASTN 2.2.27" or anyone thinks its a different problem.

thanks

Answer 1

[JC]

NCBI nt is divided in several small parts for easy download, you need all 12 pieces together.

[rehma.ar]

should i download all the pieces and join them together into one ? if so how

[JC]

just download all nt.XX.tar.gz files and uncompress all in one directory, call your Blast using "-d nt"

[rehma.ar]

thanks alot i am sure it is goona work but plz tell me one more thing as i have blast version BLASTN 2.2.21 and the latest version is "BLASTN 2.2.27"

does it have any effect on the results anyway if so should i install the new version or update

[rehma.ar]

i am sorry but it does not work when i run this for one file of database blastall -p blastn -n T -i query.fasta -d nt.01 it works perfect but when i run this for the whole database like blastall -p blastn -n T -i query.fasta -d nt or blastall -p blastn -n T -i query.fasta -d nt. or even with the wild card blastall -p blastn -n T -i query.fasta -d nt.* it does not work. plz help me

[JC]

can you copy and paste the error output please?

[rehma.ar]

when i run this command

"blastall -p blastn -n T -i query.fasta -d nt -o /blast.out"

the result is like this

Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.