Question: creating a blast database
0
gravatar for sukesh1411
2.6 years ago by
sukesh141130
South Africa
sukesh141130 wrote:

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

blast • 1.6k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by sukesh141130

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).

ADD REPLYlink written 2.6 years ago by st.ph.n2.4k
0
gravatar for Sej Modha
2.6 years ago by
Sej Modha4.1k
Glasgow, UK
Sej Modha4.1k wrote:

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.

ADD COMMENTlink written 2.6 years ago by Sej Modha4.1k
0
gravatar for sukesh1411
2.6 years ago by
sukesh141130
South Africa
sukesh141130 wrote:

Hi

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

ADD COMMENTlink written 2.6 years ago by sukesh141130
1

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.

ADD REPLYlink written 2.6 years ago by genomax63k
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