The NCBI limits the amount of compute resources that can be used when running BLAST from a single IP address. This can cause BLAST searches to run more slowly for some users, especially when running large searches or when your IP address is shared with other users.
Workaround for BLAST Searches:
We suggest either running BLAST searches directly on NCBI website, or setting up custom BLAST to run large searches locally. These options are available within Geneious by selecting the appropriate Blast Location option:
Custom BLAST:
For large searches, you can set up a local BLAST search by choosing the Custom BLAST option. This allows you to run searches on your local machine, offering more control over larger datasets.
NCBI via Website:
Use this option to perform BLAST searches directly on the NCBI website. Once the search is complete, download the results in XML format and drag-and-drop the file into Geneious to load the results.
Batch Blast
You can also submit multiple sequences from Geneious to the NCBI website.
- Select all of the sequences you wish to batch blast
- Start Blast and select the 'Blast from NCBI' option with the query set to "batch" search...
- Choose the appropriate blast database and click OK
- You should now see that the NCBI Blast website is populated with your sequences. Expand the "algorithm parameters" at the bottom and adjust the max target sequences to something appropriate (e.g. 10; this is per query).
- Once the blast completes, click Download All and choose single-file XML (see below)
- Drag this file into a new folder in geneious to get your blast hits
