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Bioinformatics algorithm enhancement blast

A Biotechnology Corporation is engaged in providing access to genomic sequence information and conducting biological research. 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.

Client

Today, with the advent of biotechnology, we can safely say that modern medicine is literally on the verge of a real revolution, which consists in the fact that instead of mass therapy, the patient will be able to receive personalized therapy modeled on a specific clinical situation.

Biotechnology, in its current formative stage, focuses on diseases for which there are currently no adequate effective therapies. In this case, we are talking about diseases that appear with age. Among them: malignant neoplasms, arthritis and neurodegenerative diseases (Alzheimer’s and Parkinson’s diseases). In addition, biotechnology offers effective therapeutic solutions in the treatment of hepatitis, multiple sclerosis and orphan diseases.

Our customer is a biotech company that turned to Azati to improve their processes.

Main Challenge

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 researchers 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 sequences.

Solution

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.

The Azati engineering team implemented the changes to the extensive BLAST algorithm code,thus making the system highly responsive to the client’s research needs.

Technologies

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SCREENSHOTS

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