The NCBI-BLAST Common URL API allows you to run searches remotely. It supports the same commands at the NCBI web server and at a cloud provider installation. This allows you to switch from running searches at the NCBI web server to a cloud provider (or visa versa) with minimal effort.
Every call to the Common URL API must include the CMD parameter, which can take one of four different arguments. You may use Put for search submission, Get for checking the status of a submission or retrieving results, Delete to remove a search and its results or DisplayRIDs to list all RIDs in the system. Each argument to CMD requires or allows certain other parameters as described in the table below. The table below lists all supported parameters. Other parameters are not supported and should not be relied upon by users of the URL API. An asterisk (*) in the CMD column indicates that the parameter is required for that command.

Also, see the information at Running Web BLAST and authentication.

Parameter Definition Type CMD Allowed values
QUERY Search query String Put * Accession, GI, or FASTA.
DATABASE BLAST database String Put * Database from appendix 2 or one uploaded to blastdb_custom (see appendix 4)
PROGRAM BLAST program String Put * One of blastn, megablast, blastp, blastx, tblastn, tblastx
FILTER Low complexity filtering String Put F to disable. T or L to enable. Prepend “m” for mask at lookup (e.g., mL)
FORMAT_TYPE Report type String Put, Get HTML, Text, XML, XML2, JSON2, or Tabular. HTML is the default.
EXPECT Expect value Double Put Number greater than zero.
NUCL_REWARD Reward for matching bases (BLASTN and megaBLAST) Integer Put Integer greater than zero.
NUCL_PENALTY Cost for mismatched bases (BLASTN and megaBLAST) Integer Put Integer less than zero.
GAPCOSTS Gap existence and extension costs String Put Pair of positive integers separated by a space such as “11 1”.
MATRIX Scoring matrix name String Put One of BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90, PAM250, PAM30 or PAM70. Default: BLOSUM62 for all applicable programs
HITLIST_SIZE Number of databases sequences to keep Integer Put,Get Integer greater than zero.
DESCRIPTIONS Number of descriptions to print (applies to HTML and Text) Integer Put,Get Integer greater than zero.
ALIGNMENTS Number of alignments to print (applies to HTML and Text) Integer Put,Get Integer greater than zero.
NCBI_GI Show NCBI GIs in report String Put, Get T or F
RID BLAST search request identifier String Get *, Delete * The Request ID (RID) returned when the search was submitted
THRESHOLD Neighboring score for initial words Integer Put Positive integer (BLASTP default is 11). Does not apply to BLASTN or MegaBLAST).
WORD_SIZE Size of word for initial matches Integer Put Positive integer.
COMPOSITION_BASED_STATISTICS Composition based statistics algorithm to use Integer Put One of 0, 1, 2, or 3. See comp_based_stats command line option in the BLAST+ user manual for details.
FORMAT_OBJECT Object type String Get SearchInfo (status check) or Alignment (report formatting).
NUM_THREADS Number of virtual CPUs to use Integer Put Integer greater than zero (default is 1). Supported only on the cloud

If a parameter is not required and not provided, then the default value will be used. That default value may depend upon the BLAST search you are running.