To ensure fair service for all customers, NCBI limits the total query length per web BLAST search. Hence, the number of sequences that you can enter in a BLAST search will depend on their lengths. For example, you can enter numerous short sequences in one search if their added length stays below the set limit.
These are the maximum allowed query lengths set by NCBI:

• 1,000,000 bp: nucleotide queries of BLAST databases using blastn, blastx, and tblastx
• 100,000 bp: protein queries of BLAST databases using blastp, and tblastn
• 10,000,000 bp: for all web BLAST suites when using the Align two or more sequences option

If you enter a query exceeding the length limit, the search will simply not run. You will receive a warning, stating that your query is too long.

Does keeping the query length below the maximum guarantee a successful search?

No. Even if you keep your query length below the required maximum, your search could still fail if it is computationally tasking. In such a case, you might have exceeded yet another imposed BLAST limit, that is the CPU allocated to each search.

 

Where can you learn more?

Related knowledge articles on web BLAST limitations, errors, and preventive measures:

• Why does my BLAST search get a “Process size limit exceeded” error?
• Why does my BLAST search get a “CPU usage limit was exceeded” error?
• How does BLAST penalize heavy usage from an IP address?
• How do I reduce search load to avoid being penalized for heavy usage when teaching BLAST in a classroom?

• Web BLAST Quick Start Guide