Question: BLAST database with local sequences
1
gravatar for Janey
12 months ago by
Janey20
USA
Janey20 wrote:

Hi I'm sorry to ask this question, maybe it's very repetitive, but i'm so confused. I want to make BLAST database with my local sequences. For this purpose, I use this command: makeblastdb -in Total.assembly.fasta -parse_seqids -dbtype nucl -out my_db After running this cammand, I get nhr, nin, nog, nsd, nsi and nsq files. Which of these files should I use in the next step? Which file is the index of my fasta file? In the next step, what command should I use to blast my sequences against this database. When I used the following command, I get error. blastn Total.assembly.fasta -query X.fasta -out results.out

Please help me

rna-seq • 830 views
ADD COMMENTlink modified 12 months ago by jrj.healey11k • written 12 months ago by Janey20
blastn -db Total.assembly.fasta -query X.fasta -out results.out

All output files from makeblastdb are used by blastn, there all part of your database (Total.assembly).

You can also look at this post : BLAST database files

ADD REPLYlink modified 12 months ago • written 12 months ago by Bastien Hervé3.7k

Hi I saw that post, but I did not understand which file should be used in next step

ADD REPLYlink written 12 months ago by Janey20
1

You will only need to point your fasta file :

-db Total.assembly.fasta

blastn will understand that you have Total.assembly.nhr, Total.assembly.nin...etc in Total.assembly location

ADD REPLYlink modified 12 months ago • written 12 months ago by Bastien Hervé3.7k

As far as I know, all those files are involved in building the database.

ADD REPLYlink written 12 months ago by Janey20

after using this command " blastn –db Total.assembly -query X.fasta -out results.out " i get this error: Too many positional arguments (1), the offending value: –db Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: –db

ADD REPLYlink written 12 months ago by Janey20
1

–db is the problem here

the "–" character is not a SHIFT + 6 character. You need to change "–" by "-"

ADD REPLYlink written 12 months ago by Bastien Hervé3.7k

Yes, I think you still need to had .fasta after Total.assembly

ADD REPLYlink written 12 months ago by Bastien Hervé3.7k

I need a correct command to blast with local database.

ADD REPLYlink written 12 months ago by Janey20

You can also read the documentation typing

blastn -help
ADD REPLYlink written 12 months ago by Bastien Hervé3.7k
1
gravatar for lieven.sterck
12 months ago by
lieven.sterck4.1k
VIB, Ghent, Belgium
lieven.sterck4.1k wrote:

To avoid lots of confusion raised here I always advice to people to use the [-out database_name] (== the basename of all your blastDB files) and for convenience also [-title database_title] options when building their blast DBs.

The value you specify for -out is what you need to provide in the blast-cmdline for -db .Default behavior is that -out is set to -in when it's not provide, hence the confusion

ADD COMMENTlink written 12 months ago by lieven.sterck4.1k
0
gravatar for jrj.healey
12 months ago by
jrj.healey11k
United Kingdom
jrj.healey11k wrote:

A BLAST database requires ALL of those files with the various extensions that your makeblastdb command produced.

For instance, if you used the command:

makeblastdb -in Total.assembly.fasta -parse_seqids -dbtype nucl -out my_db

Your database is all of the files which have the base name my_db.

When you use this in subsequent programs, you provide the file path to the location where all of these files are, e.g.

blastn -db /path/to/my_db

You don't specifiy any of the file extensions specifically.

ADD COMMENTlink written 12 months ago by jrj.healey11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1869 users visited in the last hour