blastx for multiple nucleotide sequences

Question

[harpreetmanku04]

How can I perform blastx for sequences more than 2000 in one fasta file. When I perform it on NCBI it shows no result but when I perform with single entry it perform result. And I can't do it one by one. Any solution?

Answer 1

[IsmailM]

If you are familiar with using the command line, See the BLAST+ installation notes here for more info on how to install BLAST+ on your computer and then download a BLAST database.

See this link for more information on installing and configuring BLAST+.

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If you are not familiar with the command line, I would suggest SequenceServer (only supported on Macs and Linux). This sets up everything for you (i.e. installs BLAST+ and downloads databases) and then opens up a webpage where you can then run BLAST.

To install,

gem install sequenceserver

And then to run sequenceserver

sequenceserver

This will then help you download BLAST and the BLAST database. Thereafter, it will automatically open a web browser where you can copy and paste your sequences

[harpreetmanku04]

It is nr database is present in chunks and it is taking big time to download

[IsmailM]

Firstly, please don't add a comment as an answer...

nr is indeed quite big (as such it is made of multiple files)... If you want a smaller database, have a look at SwissProt (it is a lot smaller, but it is manually curated and so contains sequences of a higher quality)...

Alternatively, you can use a remote BLAST database by using the following argument when you run BLAST+

... -db nr -remote ...

BUT beware, that the remote BLAST will take a very long time.

[harpreetmanku04]

I have downloaded nr data from ncbi ftp site one of them one folder is showing files .phr, .pin, etc exactly similar to files generated at the time of local database creation for running blastn command. What is the command for running blastx? And for creating database for blastx?

[IsmailM]

Assuming that you have blastx installed:

{blast_type}  -db #{db} -query {input_file}  -out {output_file} -evalue {e-value} -outfmt 6 -num_threads {number_of_threads}

In the above, replace all {}, with the correct values e.g.

blastx -db ../blastdb/nr -query input_seqs.fa -out input_seqs.fa -evalue 1e-5 -outfmt 6 -num_threads 8

So as you can see for the database you simply put the path to the nr database (but do not put the file ending i.e. .phr .pin etc).

I have used -outfmt 6 in the above command which will produce a tabular file - I have suggested this over other types since this is easier to analyse later (using scripts etc.)...

Be aware that this will take a long time - As a result I have gone with a lower than usual evalue so that it would be slightly faster (but nevertheless, it would still take long).

Answer 2

[Joseph Hughes]

Install the database and NCBI locally.