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Question: Makeblast db with more sequences in fasta format
1
gravatar for marghe08
3.1 years ago by
marghe08 • 10
marghe08 • 10 wrote:

Hello! I am a beginner and I need help. I downloaded from NCBI two distinct fasta files, which contain both a nucleotide sequence, and are saved in a folder on my pc; these are the names of the files: NG_006672.1.fasta NG_006682.3.fasta using locally blast would like to create a database, with makeblastdb command, which contains my 2 fasta sequences. How can I do?
blast blastdb • 1.4k views
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modified 9 weeks ago by david.prihoda • 10 • written 3.1 years ago by marghe08 • 10
4
gravatar for RamRS
3.1 years ago by
RamRS ♦ 25k
Houston, TX
RamRS ♦ 25k wrote:

Just cat the fasta file and use the concatenated FASTA file as the input to the -in argument. Here's NCBI manual on how to use makeblastdb https://www.ncbi.nlm.nih.gov/books/NBK279688/

Either cat them as a preliminary step or use the syntax -in <(cat file1.fa file2.fa) to use a subshell in the makeblastdb
ADD COMMENT • link modified 9 weeks ago • written 3.1 years ago by RamRS ♦ 25k
1

-in <(cat file1.fa file2.fa) seems not to work with Blast 2.7.1, it shows this error: BLAST options error: File /dev/fd/11 does not exist . I found out you can actually use a regular pipe like so: cat file1.fa file2.fa | makeblastdb -title myDBtitle -out myDBpath -parse_seqids

ADD REPLY • link written 9 weeks ago by david.prihoda • 10

That could be a shell restriction. If your shell allows process substitution, <() should work fine.

Also, this is a 3 year old post, so there is quite the chance the blast executable could be a different version.

ADD REPLY • link written 9 weeks ago by RamRS ♦ 25k
1
gravatar for Sej Modha
3.1 years ago by
Sej Modha ♦ 4.5k
Glasgow, UK
Sej Modha ♦ 4.5k wrote:

https://www.ncbi.nlm.nih.gov/books/NBK279688/
ADD COMMENT • link written 3.1 years ago by Sej Modha ♦ 4.5k
0
gravatar for david.prihoda
9 weeks ago by
david.prihoda • 10
david.prihoda • 10 wrote:

I found out you can just omit the -in parameter, add a -title parameter and pipe the sequences using: cat file1.fa file2.fa | makeblastdb -title myDBtitle -out myDBpath -parse_seqids
ADD COMMENT • link written 9 weeks ago by david.prihoda • 10
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