[maubp]

See http://seqanswers.com/forums/showthread.php?t=50017 for kaps's thread.

[kaps]

I think a separate thread would be a good idea for this question. See also http://blastedbio.blogspot.co.uk/201...-chimeras.html and http://www.ncbi.nlm.nih.gov/pubmed/?term=25428358

Hello Maubp,

Thanks for the blog links. i have also created a seperate thread as advised. its now called fasta files from NCBI

[maubp]

Dear all, In creating a local blast database, I downloaded fasta files from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ and http://www.ncbi.nlm.nih.gov/sites/nu...=%22Viruses%22[PORG]+AND+srcdb_refseq[PROP]. The former appeared larger than the latter, which of them is better? Do both both contain nr sequences? are they different?

Thanks

I think a separate thread would be a good idea for this question. See also http://blastedbio.blogspot.co.uk/201...-chimeras.html and http://www.ncbi.nlm.nih.gov/pubmed/?term=25428358

[kaps]

Dear all, In creating a local blast database, I downloaded fasta files from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ and http://www.ncbi.nlm.nih.gov/sites/nu...=%22Viruses%22[PORG]+AND+srcdb_refseq[PROP]. The former appeared larger than the latter, which of them is better? Do both both contain nr sequences? are they different?

Thanks

[maubp]

The simple brute force solution is make a single merged FASTA file (e.g. using the cat command), and then build a BLAST database out of that.

[poudap]

Unfortunately the $(cat Strains/*.fasta) command did not work.

The command space seperated also gave error:
BLAST options error: File Sample_no2.fasta does not exist.

[maubp]

I am wondering if you could tell me how I can make a database from different files in batch?

BLAST does not like this kind of command, where the second FASTA file is considered to be a positional argument:

makeblastdb -in Strains/example1.fasta Strains/example2.fasta -dbtype nucl -out db/stec_samples

From past experimentation, I know it will work if you quote the list of filenames making them space separated (filenames with spaces are a problem):

makeblastdb -in "Strains/example1.fasta Strains/example2.fasta" -dbtype nucl -out db/stec_samples

[rhinoceros]

This might work:

makeblastdb -in $(cat Strains/*.fasta) -dbtype 'nucl' -out db/stec_samples

[poudap]

How I can make custom database in batch?

I am wondering if you could tell me how I can make a database from different files in batch? The commands like entry_batch does not respond.
I have also used below command but it gives the error stated afterwards:

makeblastdb -in Strains/*.fasta -dbtype 'nucl' -out db/stec_samples

Error: Too many positional arguments (1), the offending value: Strains/Sample_1.fasta

P.S. A single database can be made from Sample_1.fasta with no error.

[ahmadsam]

Creating blastdb in windows

after downloading and installation
1-Use command prompt and go to the bin directory
for creating a database like protein database you need a simple multi fasta file

2- use this command :

makeblastdb -in D:\\ref.fasta -dbtype prot -out Plant

with the above code makeblastdb generate 3 file with .pin , .phr and .psq format in the bin directory.
Plant is the name of output database.

3- for using this database in sample query :

blastp -query D:\\in.txt -db plant -out D:\\Out.txt

[rhinoceros]

Hey everyone,

#I used the following to make the db

makeblastdb -in supercontigs.fasta.txt -dbtype 'nucl' -out p.full

#I then tried to run this the next step

query=NGF.fasta -db=p.full -outfmt="6" -out=blast

Any ideas how I can change my second step to successfully run the blast search?

Well for one you haven't specified a program, which should probably be blastn in your case. Second, the correct syntax would be:

blastn -query NGF.fasta -db p.full -outfmt 6 -out blast

If that still doesn't work, then I'd guess that there are problems with your environmental variables. You could go around this by specifying the paths of your program, query file, and db, i.e.

/where/is/blast/bin/blastn -query /where/is/this/fileNGF.fasta -db /where/is/this/db/p.full -outfmt 6 -out blast

optional flag you should consider: -num_threads INSERT_NUMBER_OF_CORES_IN_YOUR_SYSTEM, e.g. -num_threads 2

[maubp]

Kyle - you've left out at least part of the command you ran, and more importantly you left out important details like what the error message was. That makes it almost impossible to guess what you've done wrong.

[utagenomics]

Hey everyone,

So I am also having some similar issues. I successfully made my database in the correct folder, but then when I actually try to run my blast, it isn't working...

#I used the following to make the db

makeblastdb -in supercontigs.fasta.txt -dbtype 'nucl' -out p.full

#I then tried to run this the next step

query=NGF.fasta -db=p.full -outfmt="6" -out=blast

Any ideas how I can change my second step to successfully run the blast search?

Thanks,
Kyle

[geneart]

BLAST database

Yes, maubp ,you are correct ! I did setup the database using miRBASE mature.fa files .I was wondering if I need to format that datanase at all in doing that. It does not matter now as it worked. But I had another question again.
I have short RNA sequences from Illumina sequencer and am trying to find matches in miRBASE through a blast standalone (which has mature.fa from miRBASE to be used as a database). Now when I directly use miRBASE and use SSEARCH I get hits however when I BLST locally I don't get any hits.
I have used default parameters, which I would like to tweek to see if results change. My problem is how do I run BLASTN-short on cmd line or tweek the parameters in BLAST standalone? Any help? I looked up the BLAST manual that comes with the standalone but could not find it.
I am not that command line savy so hoping someone can suggest ways of doing it ?
Thanks in advance
Geneart.

[maubp]

Hi geneart, I'm having trouble understanding your question. Are you saying you've downloaded a FASTA file from miRBASE and want to turn this into a database? If so yes, you should use the makeblastdb command.

You can search directly against a FASTA file, but it is slower (and only uses one CPU), but will also give you pairwise e-values which will look more impressive than they really are, see:

http://blastedbio.blogspot.co.uk/2012/05/blast-ingoring-search-space-size-for-e.html