ABSTRACT

Objectives: The next-generation sequencing techniques have enabled us to retrieve massive pieces of information from online biological databases, but it has been challenging to process multiple and unlimited size expressed sequence tags files for identifying and characterizing simple sequences repeats. Many web-based tools were designed but with time due to lack of server maintenance, they become unusable; also few available stand-alone tools lack processing adequateness. Therefore with intent to process multiple expressed sequence tag files without size limits, using proper validations and ability to retrieve more genome-related features; a simple to use, speed efficient, and portable standalone tool has been developed. The front end has been designed using swing components in Java Net Beans and the entire algorithm was implemented in Java using modular object oriented approach. Interactive microsatellite search algorithm blended with dictionary based approach algorithm MISA –a Perl script was called via command line for data mining from expressed sequence tag files. Another parallel module retrieves additional information from GenBank files. In the pipeline primer 3 was invoked for designing batch primers. This algorithm with extended interface in Java Net Beans provides naïve users with a simple interactive tool for mining microsatellites, statistical analysis, primer designing, and options of BLAST programs on one platform in the form of the stand-alone application. The number of repeats/ interruptions and BLAST algorithm parameters can be reset through the graphical interface. This tool has interactive modules that provides proper validation, batch processing and cost-effective analysis of simple sequence repeats in expressed sequence tags as compared to peers and the source code can be upgraded in future as per requirements. Keywords: BLAST, Data mining, EST sequence, Java pipeline, Microsatellites, Primer Design
Publication date: 25/01/2022

https://ijbpas.com/pdf/2022/January/MS_IJBPAS_2022_JAN_SPCL_2_2005.pdf

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https://doi.org/10.31032/IJBPAS/2022/11.1.2005