Office of Technology Transfer – University of Michigan

miBLAST: Scalable Evaluation of a Batch of Nucleotide Sequence Queries with BLAST

Technology #3170

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Jignesh M. Patel
Managed By
Drew Bennett
Associate Director - Software Licensing 734-615-4004


There are times when biologists need to search a large number of short DNA sequences. BLASTing a few sequences is not a problem since it can be easily done in NCBI’s BLAST web servers or in your machine quite quickly. However, matching large number of queries can be very expensive in both effort and time necessary to run the searches.


To process a large amount of queries, U of M researchers developed an algorithm, called miBLAST. At the core, miBLAST employs q-gram indexing and filtering algorithms for fast homologous region detection between query sequences and database sequences, resulting in a substantial increase in overall performance. Note that miBLAST is not a replacement for NCBI BLAST. Rather, it is specialized for a certain type of BLAST search. For instance, miBLAST can process only nucleotide sequences and it is particularly useful in handling batch processing containing a large number of short query sequences.

Applications and Advantages


  • BLASTing large amount of nucleotide sequence queries against a central database


  • Faster and easier processing of the queries
  • Improved performance of the search