NCBI BLAST REST Java example

Question

[sureshhewabi]

Hi,

I want to BLAST multiple genes with the entire nr database, but my query is a very broad one which should return me thousands of matching records. I found following options:

• BLAST+ command-line local blast - handling nr database is too much overhead for my purpose.
• BLAST+ command-line remote blast - since query is a broad one, I got an error saying CPU limit is exceeded
• AWS BLAST server - This would be again too much effort and cost me

I would like to implement this in a fashion of restful web services. I found that EBI providing such a solution. Link: http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_rest

I have two questions:

1. Can I use NCBI BLAST REST to blast multiple genes with the entire nr database?
2. Where can I find a tutorial or example to implement NCBI BLAST REST in Java?

Note: I have tried BioJava, it didnt work for me

Thanks

[Brian Bushnell]

What kind of computational resources do you have locally? Meaning, disk space, core count, and RAM.

[sureshhewabi]

I have iMac 2.5 GHz Intel Core i5, 16GB RAM. Nr.gz database is around 23GB.

I am doing this blast to build a software. so anyone should be able to do the blast in their computer which is not feasible with local blast.

In other words, I want in incorporate blast functionality into my software programme I am writing.

[Brian Bushnell]

Clearly, you can't host the whole reference locally. Have you considered alternatives like MinHashSketch? Actually, what is your goal?

[sureshhewabi]

My goal is to find homologous sequences for each gene.