New BLAST default parameters and search limits coming in September

To provide a more efficient BLAST experience for everyone, we’re changing some parameters and limits on the web BLAST service on September 8, 2020. The new settings, listed below, will improve overall performance and make search times more consistent.

  1. The Expect Value Threshold default setting will be reduced to 0.05.
  2. The maximum number of target sequences (Max target sequences) limit will be no more than 5,000.
  3. The maximum allowed query length for nucleotide queries (blastn, blastx, and tblastx) will be 1,000,000 and 100,000 for protein queries (blastp and tblastn).

These changes will help keep the BLAST service running smoothly as the already very large databases continue to grow rapidly. If you have any questions or concerns, please email us at

16 thoughts on “New BLAST default parameters and search limits coming in September

  1. the old version suited me for work, and the new one was not convenient. too short nucleotide sequences can be analyzed with a new version

  2. I received a message telling me I had to change the “filter” settings in order to receive a BLAST result. I don’t see the term “filter” anywhere on the search page, so don’t know how to change the settings. I am receiving a “no significant match found” message, and this seems wrong since this is a sequence I have used before without any problem.

  3. I find this frustrating. I want to use the gene for myom1 and see if predicted motifs align. My motifs have a probability to bind the 3’UTR but they may bind anywhere. My gene is 4,000 bp and it won’t let me align with anything over 1,000 bp

  4. It’s not working. Gives me this error.
    Message ID#36 Error: Cannot validate the Blast options: Greedy extension must be used if gap existence and extension options are zero

    Yesterday, it was fine.

  5. This new version does not work well as the before, really! I can not blast a DNA fragment within the frame of a genome sequence. For example, I want to balst a sequence within the genome of S.cerevisiae, however, it show any similarity, however, in the previous version, it has some similarity.

  6. I have noticed that e-value variable is inconsistent when calculated by a BLAST+ search. Is use the blast_formatter program for retrieving different outputs from my blast search. However, retriveing just evalues (“-outfmt 7 evalue”) gives me different e-values than the ones given on the alignment output (“outfmt 0). This gives me some problems as I want to filter hits by evalue. What is the reason for this discrepancy?

      1. Dear NCBI staff. I have already been in contact with Tao Tao who has resolved the issue. It was a misunderstanding on my site. Best,

Leave a Reply