BLAST multiple sequences against each other from one FASTA file

Question

[Keely]

Hi,

I am a beginner to using BLAST locally on Mac OSX. I have downloaded ncbi-blast-2.2.31+.dmg and have installed it. I have a FASTA file with multiple protein sequences in it and am trying to BLAST each sequence against every other sequence within that FASTA file as I am looking for duplicates. I am also a beginner to programming and am struggling to get my head around using the Terminal. I'm not really sure where to start. I've tried making a BLAST db from my FASTA file using

makeblastdb -in sequence.fasta -dbtype prot -out sequence -title -sequence

and it seems to have worked but I can't find the results anywhere.

I'm not even sure this is the right path to take.

Can anyone please help set me on the right path?

Keely

[Nelo]

Hey

How did you make blast db

Answer 1

[Pierre Lindenbaum]

Once your blast database was created, you just have to run blastp the original fasta against the compiled database.

blastp -query sequence.fasta -db sequence -out result

[Keely]

Thanks Pierre, but when I try to do the blastp this is what I get:

blastp -query sequence.fasta -db sequence
BLAST Database error: No alias or index file found for protein database [sequence] in search path [/usr/local/ncbi/blast/bin::]

When I do:

blastp -query sequence.fasta -db sequence -out result

I get:

Command line argument error: Argument "out". File is not accessible:  `result'

[kozhaki.seq]

Here is how my note on BLAST run,

Make a directory, enter the directory. Keep database file and input file inside it.

1. Make index files for the database : makeblastdb -in indica.fasta -dbtype prot -out indica
2. Blast your sequence against the database: blastp -query japonia.txt -db indica -out alignment.txt -outfmt 7

[Keely]

I made the database as follows:

makeblastdb -in sequence.fasta -dbtype prot -out sequence

Building a new DB, current time: 10/04/2015 18:20:03
New DB name:   /usr/local/ncbi/blast/bin/sequence
New DB title:  sequence.fasta
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B

Adding sequences from FASTA; added 227 sequences in 0.0208449 seconds.

I then created a alignment.rtf file from textEdit and then tried to blast my sequence against the database and I get the same problem:

blastp -query sequence.fasta -db sequence -out alignment.rtf -outfmt 7
BLAST Database error: No alias or index file found for protein database [sequence] in search path [/usr/local/ncbi/blast/bin::]

[vladimir.khramkov]

specify full path to blast databse you just created

best practive is to put database files into ./db directory - in your case into /usr/local/ncbi/blast/db

1. mkdir /usr/local/ncbi/blast/db
2. makeblastdb -in sequence.fasta -dbtype prot -out /usr/local/ncbi/blast/db/sequence
3. blastp -query sequence.fasta -db /usr/local/ncbi/blast/db/sequence

[Keely]

I tried making a directory called db to store the database, but it won't let me even though I have full administrator rights:

mkdir /usr/local/ncbi/blast/db
mkdir: /usr/local/ncbi/blast/db: Permission denied

[vladimir.khramkov]

Ok, then try to create directory in the home

mkdir -p ~/blast/db
makeblastdb -in sequence.fasta -dbtype prot -out ~/blast/db/sequence
blastp -query sequence.fasta -db ~/blast/db/sequence

[Keely]

Thank you! I think I've got it working now :)