Drop us a line
If you are interested in the development of a custom solution - send us the message and we'll schedule a talk about it.
Azati Software
Multiple sequence search
A Life Science Portal was endowed with extensive search capabilities with a view to helping the scientific community in their analyses and research activities, providing the functionality to search with multiple entry sequences across various nucleotide and peptide databases.
CUSTOMER
Biotechnology is a broad range of technologies that employ living organisms or parts of them to make diverse products. For example, drugs and therapeutics, nutritional compounds, environmentally friendly chemicals and materials, biofuels, and novel functional materials can be produced through biotechnology. More broadly, medical biotechnology, agricultural biotechnology and industrial biotechnology will all play increasingly important roles in our everyday life. Biotechnology can also be employed to degrade toxic or harmful chemicals and agents to solve environmental problems.
Our customer is a huge biotechnology corporation that involves Azati in the development and enhancement of multiple sequence search.
Objective
Research carried out in the biotechnology industry is based on a preliminary study of information. A variety of methods can be used to obtain data, but when there are too many of them in the database, it becomes almost impossible to do it manually in time. Thus, the Azati main task was to achieve the ability to search for several consecutive queries, capable of structuring the interrelated elements and allowing their analytical and research activities to be carried out.
Challenge
Biological scientists, engaged in searching for complementarity determining regions (CDRs), fusion/chimeric constructs, recombinant plasmid constructs and bispecific antibodies, were in need of a reliable tool, which would enable search for multiple nucleotide (or protein) queries against the nucleotide (or protein) database. The challenge was risen due to the question of the project feasibility, as the tool for searching with several query sequences at that time hadn’t been introduced before.
Solution
Azati team designed, developed and released a general purpose Multiple Sequence Search (MSS) tool, than can accept and search on up to six query sequences. The MSS tool can be used to find and list documents that contain CDR sequences of interest. Also, one may perform a simultaneous search on multiple CDRs contained within the same patent document, taking into consideration that the CDRs might be present in different claims. The MSS tool uses our enhanced version of the Smith-Waterman algorithm in order to produce not only accurate and comprehensive results, but also do it in a considerably shorter time (30 to 50 times) than the standard Smith-Waterman algorithm.
The interface makes it easy to track and see whether there is one or more than one similar sequence that might have been claimed within a single document. An advanced scoring system was designed to assign a higher score to those documents that contain a greater number of CDRs matching the search query, which produces more relevant results. The system also provides an option to show combined alignment. We also implemented a functionality to generate the reports (of 4 different file formats) based onthe search results, allowing the users to clearly identify which query sequences are being aligned to the subject ones. The created Multiple Sequence Search algorithm fully satisfies the requirements set and brings a higher degree of sophistication to the researchers.
Technologies
SCREENSHOTS
Featured case studies:
JavaScript, Ruby
HR Planning SoftwareThe customer asked Azati to audit the existing solution in terms of general performance to create a roadmap of future improvements. Our team also increased application performance and delivered several new features.
Python
Stock Market Trend Discovery with Machine LearningAt Azati Labs, our engineers developed an AI-powered prototype of a tool that can spot a stock market trend. Online trading applications may use this information to calculate the actual stock market price change.
Python
Semantic Search Engine for Bioinformatics CompanyAzati designed and developed a semantic search engine powered by machine learning. It extracts the actual meaning from the search query and looks for the most relevant results across huge scientific datasets.
Java, JavaScript
E-health Web Portal for International Software IntegratorAzati helped a well-known software integrator to eliminate legacy code, rebuild a complex web application, and fix the majority of mission-critical bugs.
JavaScript, Ruby
Custom Platform for Logistics and Goods TransportationAzati helped a European startup to create a custom logistics platform. It helps shippers to track goods in a real-time, as well as guarantees that the buyer will receive the product in a perfect condition.