creating a blast database

Question

[sukesh1411]

Hi

I downloaded the nr.gz file from blast ftp link. nr folder has 44 tar.gz files. I could not make a blast database using this folder. Can anyone help me to create a database for doing blast.

Command i used to create a blastdb makeblastdb -in nr -input_type fasta -dbtype prot -title nrprotein -parse_seqids -out proteindbncbi

Building a new DB, current time: 08/23/2016 15:27:08 New DB name: proteindbncbi New DB title: nrprotein Sequence type: Protein Keep Linkouts: T Keep MBits: T Maximum file size: 1000000000B BLAST options error: File nr.00 does not exist

[st.ph.n]

What did you do with the 44 tar files? Did you unzip them? Your in file is "nr" in your command, but your blast error is looking for nr.00 (the first of the db files).

Answer 1

[Sej Modha]

You can download pre-formatted BLAST db from NCBI ftp and automatically update them using update_blastdb.pl utility. For more info check out my blog.

Answer 2

[sukesh1411]

Hi

sorry I could not perform the above task because i could not install the bioperl.

[GenoMax]

Please use ADD COMMENT/ADD REPLY when replying to existing posts. SUBMIT ANSWER should be reserved for new answers to original question. This comment belongs up against @Sej's post if you are responding to that post.