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How to: Submit multiple query sequences in a single BLAST search

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  1. Choose the appropriate BLAST service from the BLAST Homepage.
  2. Enter NCBI sequence identifiers (accession numbers, gi numbers) or FASTA-formatted sequences in the appropriate text box.  Please note that multiple query sequences are allowed, but be sure to include the list of identifiers (accession or gi numbers) as one per line or the group of FASTA sequences with each beginning on a new line and starting with the greater-than sign (">").
  3. Local files of sequences or identifiers formatted as described above may be submitted using the "upload file" feature on the submitting form. Click "Browse" to find and choose the local file.
  4. Click the "BLAST" button to submit the search. There is a processing time limit (CPU limit) on Web BLAST searches. The limit may be exceeded by batch submissions. If this happens, reduce the number of sequences submitted in a batch; see this BLAST FAQ.


  1. Download a BLAST+ package from the BLAST download page. These are command line applications; no graphical interface is available.
  2. One of the command line options is “-remote”, which sends the search to NCBI BLAST servers, avoiding the need to install and maintain local databases.
  3. The "-remote" function in BLAST+ is the recommended replacement for Netblast (blastcl3) in legacy BLAST.