Sequence Alignment Algorithm Enhancement

Bioinformatics Algorithm Enhancement



A Biotechnology Corporation is engaged in providing access to genomic sequence information and conducting biological researches. In order to beat off the challenge associated with short sequence searching, the company turned to Azati with the request to optimize the BLAST algorithm they use.


Biotechnology Corporation


One of the research teams of our client company is dedicated to working with primers, which are short strands of DNA/ RNA used in the polymerase chain reaction or hybridization. For biological sequence comparison the researches use BLAST algorithm.

The problem lies in the fact that the matches, significant to the query sequence, are often not found under the standard BLAST settings. Being a probability based algorithm, BLAST omits a considerable amount of sequences when conducting a sequence search with a short query sequence (less than 20 bases). The reason for this is that the significance threshold is set too stringently, and the default sequence length parameter is set too high. Thus, BLAST was failing to provide the necessary level of accuracy to the researchers.

The client was in need of BLAST algorithm customizations to gather more accurate results from searches with short query sequence.


By having strong technological skills and deep domain knowledge in bioinformatics, our development team elaborated the algorithm parameters and additional search filters, which specifically address the issues of the searches with short query sequences. The system was redesigned to automatically adjust these developments: the preset values on the search launch page help to provide optimum results.  Azati engineering team implemented the changes to the extensive BLAST algorithm code, thus making the system highly responsive to the client’s research needs.


  • C/C++

Some detailed information not disclosed due to NDA restrictions