We are happy to announce the release of BESTSeq search (beta-version) on the SequenceBase Research Portal!
The new BESTSeq search is aimed to discover nucleotide and protein sequences with the exact sequence similarity. It is ideal for prior art searching, which include Patentability, Patent Validity and FTO searches.
FASTA, BLAST and Smith-Waterman have limited effectiveness in finding the precise alignment. BESTSeq search has different logic – it searches out the best way to fit the whole submitted sequence into the subject one.
Advantages of BESTSeq search over BLAST
- 100% Complete and Accurate Results
We modified 6 out of 30 residues of a sequence:
Then launched Blast and BESTSeq searches and get the following results:
Blast failed to find the original sequence, though the real percent identity is 80%.
BESTSeq search successfully found the original sequence:
Therefore, if you want to know which sequences in the database have 80% or more nucleotides in common with your query sequence, BESTSeq search is the ideal tool to find the right answer.
- Reproducible Results
Blast is based on heuristics. It doesn’t report all alignments it finds – only those that the algorithm finds more relevant compared to the others. Therefore, if the database grows, there are high chances of your previous results disappearing the next time the same search is done.
Unlike Blast, BESTSeq search has no heuristic shortcuts.
When assessing the relevance of alignment, it relies on the number of differences, e.g. mismatches and indels for every sequence pair in particular. When the same search is done even after the database update – the previously found sequences won’t ever disappear, as the newly added sequences make no difference to the algorithm’s assessment routine.
This way the BESTSeq always provides reproducible answers.
If you are not yet a SBRP subscriber you can arrange for a free trial by contacting firstname.lastname@example.org.
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