Searching for sequence similarities using BLAST

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The Basic Local Alignment Search Tool (BLAST) finds regions of similarity between sequences, comparing nucleotide and protein sequences to calculate the statistical significance of matches. Use BLAST to infer functional and evolutionary relationships between sequences and identify members of gene families.

Search sequences using BLAST

You can use BLAST algorithms to find DNA and AA sequences in your Benchling inventory based on their similarity to an input sequence. The search returns matching sequences and their similarity scores based on the selected algorithm.

To search for a sequence:

  1. Right-click a sequence selection and select Run Benchling BLAST.
    • Alternatively, you can click the lens icon in the left-side menu to open global search, then click the DNA helix in the search bar to open the BLAST modal.
  2. In the BLAST modal, select the BLAST algorithm you're using, then select the input sequence using one of these methods:
    • Select the entities in Benchling
    • Enter or paste the sequences in the text box
    • Upload a file of the sequences, using an approved format
  3. [Optional] Select the parameter values to customize your query. View the list of parameters and their effects at the National Library of Medicine website.
  4. Click Run BLAST. The modal will close and the search launches in the global search panel. Note that some search features, like filters, are disabled when using BLAST.

Use the information to the right of the Authors column to compare the similarities of each returned sequence to the input sequence and select the best candidate for your next steps.


What BLAST algorithms are available?

At this time, supported algorithms are:

  • blastn
  • blastp
  • blastx
  • tblastn
  • tblastx

Can I use BLAST to find sequences in external databases?

No. BLAST only searches sequences in your Benchling inventory.

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