This page describes how to use the NCBI-BLAST Common URL API to run remote BLAST searches. These instructions assume you are running searches at a cloud provider, but minor modifications allow you to run searches at the NCBI web server. A note at the bottom of this page provides information on searches at the NCBI.

To run a search, you should:

  1. Launch a BLAST instance. The security group must allow access through HTTP. If possible, restrict the allowed IP’s for HTTP so as to include only those of the intended users. See setting up remote access and your cloud provider’s documentation. The examples on this page assume Amazon Web Services (AWS).

  2. Once the instance has launched, obtain the Public DNS from your cloud provider. For AWS, the Public DNS will look like: though the exact numbers and letters will be depend upon your instance.

  3. Launch a search using your Public DNS plus cgi-bin/blast.cgi. You will need to authenticate before submitting a search. For the example Public DNS given above, a URL to search the sequence of accession u00001 against nt would be:

  4. The server will respond with HTML containing a QBlastInfo block. The QBlastInfo block will contain a RID (“Request ID”) that can be used to retrieve results as well as a RTOE that is an estimated time in seconds until the search is completed. An example QBlastInfo block is:

        RID = SYZDXEWK014  
        RTOE = 31  
  5. You may check the status of the search by invoking blast.cgi with the parameters CMD=Get, FORMAT_OBJECT=SearchInfo, and RID=VALUE, where VALUE is the RID returned by the server. The server will respond with a page containing a QBlastInfo block with the status set as one of WAITING, UNKNOWN, or READY.

  6. Once the search is finished, you may retrieve results by invoking blast.cgi with the parameters CMD=GET and RID=VALUE, where VALUE is the RID the system returned. An example would be “CMD=Get&RID=6NTRF1YLO8”. You may also specify the report type (e.g, add FORMAT_TYPE=Text).

Note: If you have not restricted your security group, anybody with knowledge of your public DNS can use CMD=DisplayRIDs to see all remote searches available on the system.

Note: The BLAST server at the NCBI supports the same URL API. At the NCBI, you should use the URL but follow the same basic procedure. Naturally, you do not need to launch an instance first. Note that only HTTPS is supported at the NCBI server after 09/30/2016. The NCBI BLAST server is a shared resource and usage restrictions may apply. See information here.