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NCBI BLAST REST Java example
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19 months ago
Sri Lanka

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

blast REST Java • 1.1k views
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What kind of computational resources do you have locally? Meaning, disk space, core count, and RAM.

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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.

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

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My goal is to find homologous sequences for each gene.

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