How can I write a bash command to blast local nt database?

[hyates]

I have been reading this.

I was able to write a basic query using blast n as follows:

blastn -db ~/programming/blastexample/db/tdb -query ~/programming/blastexample/db/even_tribolium.fasta

It seems to me that I must replace tdb (I used makedb to create this) with the downloaded local nt database?

However, I now downloaded nt into local database and I have the following questions:

• How can I blast my fasta file against local nt blast database?
• Are there options only to output the species name, contig, and E-value?
• Where did my nt local blast database go? ha ha ha.

Thanks for considering my question and your patience. I am very new to all of this.

[GenoMax]

Originally Posted by hyates

I have been reading this.

I was able to write a basic query using blast n as follows:

blastn -db ~/programming/blastexample/db/tdb -query ~/programming/blastexample/db/even_tribolium.fasta

It seems to me that I must replace tdb (I used makedb to create this) with the downloaded local nt database?

However, I now downloaded nt into local database and I have the following questions:

• How can I blast my fasta file against local nt blast database?
• Are there options only to output the species name, contig, and E-value?
• Where did my nt local blast database go? ha ha ha.

Thanks for considering my question and your patience. I am very new to all of this.

Some questions for you:

1. Did you download all pre-formatted nt.nn.tar.gz files from this link: ftp://ftp.ncbi.nlm.nih.gov/blast/db/ and unzip them in a single directory. Do not do anything else to the files. This database is pre-formatted.

When using the database provide -db /path_to/nt (do not worry about file numbers).

2. Output options for blast: http://www.ncbi.nlm.nih.gov/books/NB...BLAST_search_r
If you don't like what you see there are custom parsers available to get just what you need.

[hyates]

Originally Posted by GenoMax

Some questions for you:

1. Did you download all pre-formatted nt.nn.tar.gz files from this link: ftp://ftp.ncbi.nlm.nih.gov/blast/db/ and unzip them in a single directory. Do not do anything else to the files. This database is pre-formatted.

When using the database provide -db /path_to/nt (do not worry about file numbers).

2. Output options for blast: http://www.ncbi.nlm.nih.gov/books/NB...BLAST_search_r
If you don't like what you see there are custom parsers available to get just what you need.

• I ran ./update_blastdb.pl nt but I don't think I specified a directory. Oh no...
• Thanks for the link to options. I am hopeful it has what I need since I am asking for basic fields.

[GenoMax]

Originally Posted by hyates

• I ran ./update_blastdb.pl nt but I don't think I specified a directory. Oh no...

This would be a large download. So depending on bandwidth available it could take some time. Make sure you have enough space available on disk and do not do this via wi-fi

[hyates]

Originally Posted by GenoMax

This would be a large download. So depending on bandwidth available it could take some time. Make sure you have enough space available on disk and do not try this on wi-fi

Thanks. I think I tried this before and put it in the directory with update_blastdb.pl, so I moved the files to a new directory. However, I am rerunning the command into a directory I wish for it to be in.

So, in theory, this command should work with the local blast nt I download, right? In otherwords, blast my fasta file against the local nt database?

blastn -db ~/path/to/my/local/nt/db -query ~/path/to/this/fasta/even_tribolium.fasta

[GenoMax]

Originally Posted by hyates

Thanks. I think I tried this before and put it in the directory with update_blastdb.pl, so I moved the files to a new directory. However, I am rerunning the command into a directory I wish for it to be in.

So, in theory, this command should work with the local blast nt I download, right? In otherwords, blast my fasta file against the local nt database?

blastn -db ~/path/to/my/local/nt/db -query ~/path/to/this/fasta/even_tribolium.fasta

You minimally want something like this, if you want click-able html output:

$ blastn –query ~/path/to/this/fasta/even_tribolium.fasta -db /path_to/nt -task blastn -html -out out.html