New version now available
Do you use NCBI’s standalone BLAST tool (BLAST+)? The latest version of BLAST+ is now available and includes two exciting new features! You can now run searches faster and focus your searches by organism more easily.
What’s new?
Run searches faster
BLAST+ now runs 2-10x faster for small databases and large numbers of queries when you use multiple threads (CPUs) by automatically selecting the fastest mode for your search. Get more details.
Focus your search by organism
Limit your search to sequences from a group of organisms without first using a custom script to get all Taxonomy IDs (taxids) for the group. You can use NCBI’s Taxonomy to lookup taxids for taxonomic groups.
Get faster and focused search results simultaneously
These two new features can work together to deliver more targeted and even faster search results. When limiting your search by organism, you’re searching a smaller database. Often this means the database size is small enough that BLAST can automatically switch to a faster search mode, and the organism limit means you only see relevant matches.
Example
The command-line example below combines multi-threading (-num_threads 16) and an organism limit that restricts the search to sequences from bacterial genus Helicobacter (-taxid 209). See the BLAST® Command Line Applications User Manual for more information on command-line options.
Generic command-line
[blast program] -db [database name] -query [your query filename] \ -num_threads [integer] \ -taxids [taxid number] -out [your output filename]
Example command-line
blastn -db nt -query sampleQueryFile.fa -num_threads 16 \ -taxids 209 -out H_pylori.out
Learn more
For more information about BLAST+ and for step-by-step instructions on how to use it, check out our BLAST User Manual.
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