dBLAST Computer Software for Biological Database Sequence Similarity Searching

dBLAST is a software system for laptop/desktop computer utilization as this software can be downloaded easily and run on computers. BLAST is an already available online tool which is used for the local sequence alignment of two sequences, but there are certain features which are not available in BLA

Project Title

dBLAST Computer Software for Biological Database Sequence Similarity Searching

Project Area of Specialization

Software Engineering

Project Summary

dBLAST is a software system for laptop/desktop computer utilization as this software can be downloaded easily and run on computers. BLAST is an already available online tool which is used for the local sequence alignment of two sequences, but there are certain features which are not available in BLAST. This lead us to design the desktop version of BLAST which will help users in many ways like automatic sequence conversions, sequence alignments without continuous internet supply, saving the alignment and individual sequences for further utilization. The method employed for software development involves various steps including planning, designing, coding, implementation and maintaining the software system.

The software system was designed using Waterfall schema and the language utilized was Java in which the package BioJava through which the module Qblast API was utilized for database searching against the NCBI databases. ECLIPSE IDE (Integrated Development Environment) was utilized for the development of the software system along with the framework SWING FX for the designing of the interface for the software. The output of the software system are HTML files of the entire search results analysis from BLAST as well as the ability to save the search results for later use.

The software system was planned as no desktop application is solely developed for sequence alignment. The system is designed while making ensured that software system will not depend on any type of linked browser for sequence similarity instead it will directly connect with BLAST API. In online version of BLAST only sequence format which is readable is FASTA, this software will have automatic sequence reading based on file given for alignment and will convert it in FASTA from other formats. The software system is designed to have long-Term Storage option which is missing in online BLAST and only provide saving of result for 24 hours. One more feature which is not available previous BLAST is downloading of individual sequences, but this system software will provide the option of saving individual sequence data involved in alignment. This software system will utilize less memory as no browser is needed to perform task. Notification will inform about completion of alignment will the user is away which is also missing in previous BLAST. All these things which must be included in original BLAST and are missing have been tried to address here for better alignment tool development.

Project Objectives

1. Sequence conversion facility based on sequence file reading.
2.  Can be used without internet facility as stand-alone program, once downloaded.
3. Long-term history providing as compared to online version as that has Short-term history.
4. Less memory consumption
5. Time efficient
6. Notify the user when task is accomplished.

Project Implementation Method

• Project will be implemented using Java as Coding Language.
• The package utilized is BioJava.
• The framework used is Swing FX.
• The software used for compilation, running and debugging is Eclipse.
• API-BLASTq is utilized for the alignment.

Benefits of the Project

• The major benefit of this software system is that it is executable through the operating system without an internet connection and can help in analysis of the search results without the use of an internet connection.
• It allows the user to have their DNA/RNA/protein sequence converted into a FASTA format automatically.
• It allows the user to download the individual sequences from the search results that show any similarity against the query sequence.
• It has an integrated notification system that uses Windows Notification System to alert to the user that their results are ready to be visualized and analyzed.
• It lies at the center of all the Bioinformatics related research and will be very useful for the researchers because a browser isn’t required for the database searching and it reduces the timeframe for the database searching to take place.

Technical Details of Final Deliverable

Minimum System requirements are:

1. 200 Mb Storage
2. 1 GHz Processor
3. 512 Mb RAM
4. Internet facility for downloading software system

User will receive following files after job completion:

1. HTML files of results
2. FASTA files for individual sequences
3. Alignment files

Final Deliverable of the Project

Software System

Core Industry

Others

Other Industries

IT

Core Technology

Cloud Infrastructure

Other Technologies

Others

Sustainable Development Goals

Industry, Innovation and Infrastructure

Required Resources

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