Recently introduced BESTSeq search (previously named as IP-search) is a new algorithm elaborated at SequenceBase Corporation. The new searching tool is intended for discovering nucleotide and protein sequences with the exact sequence similarity. It is ideal for prior art searching, which include Patentability, Patent Validity and FTO searches.


Blast vs Smith-Waterman vs BESTSeq

BLAST and Smith-Waterman have limited effectiveness in finding the precise alignment. BESTSeq has different logic – it searches out the best way to fit the whole submitted sequence into the subject one.

The full comparison of these algorithms is represented in the table below:

2018-06-04-BESTSeq - Clarivate presentation (1).pdf ‎- Microsoft Edge


How many results does BESTSeq return compared to Blast or Smith-Waterman ?

BESTSeq returns more results than Blast and around the same number as SW does. However, one should consider the following:

  1. Each algorithm has different scoring approach. As for BESTSeq, it makes more significant (from IP researchers perspective) results appear on top.
  1. BESTSeq cuts out the insignificant results by % Identity threshold. Changing this number to a lower value will produce more results. This can be done at a step of launching a search in the algorithms parameters settings:





Enjoy the convenience and high-quality searching, analytic, and reporting tools the SequenceBase Corporation offers!

You can arrange for a free trial by contacting (if you already have a subscription to Geneseq, please make a note in your email). Also,you can leave feedback or ask any question via contacting