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SEDA: A Desktop Tool Suite for FASTA Files Processing.

Hugo Lopez-Fernandez, Pedro Duque, Noe Vazquez

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |November 25, 2020
    PubMed
    Summary

    SEDA (Sequence Dataset builder) is a desktop application simplifying DNA and protein sequence data manipulation for researchers. It offers advanced bioinformatics tools, easing dataset preparation for phylogenetic and phylogenomic studies.

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    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Genomics

    Background:

    • Life science researchers frequently work with large DNA and protein sequence datasets.
    • Existing bioinformatics tools may lack user-friendly interfaces or comprehensive functionalities for sequence data manipulation.
    • A need exists for accessible tools that support researchers without programming expertise.

    Purpose of the Study:

    • To introduce SEDA (Sequence Dataset builder), a multiplatform desktop application designed for efficient FASTA file manipulation.
    • To demonstrate how SEDA can be used to build data handling protocols and prepare high-quality datasets for various biological studies.
    • To highlight SEDA's user-friendly features and advanced utilities for bioinformatics tasks.

    Main Methods:

    • Development of a multiplatform desktop application with a graphical user interface.
    • Integration of simple (filtering, sorting, reformatting) and advanced (BLAST, domain annotation, alignment) utilities.
    • Provision of easy-to-install versions, including a Docker image, and comprehensive documentation.

    Main Results:

    • SEDA provides a user-friendly platform for manipulating DNA and protein sequences in FASTA format.
    • The application includes advanced bioinformatics utilities not commonly found in similar software.
    • SEDA facilitates the preparation of datasets for phylogenetic, protein family characterization, and phylogenomic studies.
    • The software efficiently handles large datasets and is accessible to users with no programming skills.

    Conclusions:

    • SEDA empowers life science researchers by simplifying complex sequence data management and analysis.
    • Its comprehensive features and user-centric design make it a valuable tool for bioinformatics tasks.
    • SEDA is an open-source solution, readily available for academic and research purposes.