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Set up a blast remote server

I know that blastp has a -remote option, which allows you to run your query on NCBI servers (see here).

Is there a way I can set up my own remote server that could be queried using blastp and would run queries against my own custom database? I am running lots of blastp queries on a cluster of machines, and I think it would be much faster if I delegated this work to a single machine that could use a local blast database, instead of querying a database stored on a distributed file system?

blast
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updated by Jeremy Leipzig Jeremy Leipzig • written by ostrokach ostrokach

3 answers

Check the documentation for NCBI BLAST AMI. While this is talking about enabling remote blast on AMI, the idea should be similar for local implementation.

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written by GenoMax GenoMax

You can transform any local FASTA file into a blast database, by using the makeblastdb command.

$ makeblastdb -h
USAGE
  makeblastdb [-h] [-help] [-in input_file] [-input_type type]
    -dbtype molecule_type [-title database_title] [-parse_seqids]
    [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
    [-mask_desc mask_algo_descriptions] [-gi_mask]
    [-gi_mask_name gi_based_mask_names] [-out database_name]
    [-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]
    [-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
   Application to create BLAST databases, version 2.6.0+

Use '-help' to print detailed descriptions of command line arguments
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written by st.ph.n st.ph.n

OP is asking if he can setup --remote functionality (which normally uses NCBI) on local hardware.

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written by GenoMax GenoMax

I think it would be much faster if I delegated this work to a single machine that could use a local blast database, instead of querying a database stored on a distributed file system

I must've interpreted this wrong, then.

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written by st.ph.n st.ph.n

He wants to do that but additionally allow --remote access to node/server containing the database.

That said I am not sure if a local database would be faster than one on a distributed file system (assuming it was properly setup). Subject to what distributed file system really translates to in OP's case.

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written by GenoMax GenoMax

I wrote this wrapper nearly a decade ago but it should still work https://github.com/leipzig/blast-wrapper

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written by Jeremy Leipzig Jeremy Leipzig

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