[Next-Generation Sequencing Book]
  • [Photo] J.W. Bizzaro • December 23, 2004
    bioFOX [1] would probably complement BioBar [2] very nicely on your Mozilla browser. From the website:

    Code bioFOX aims at implementing various bioinformatics tools as an extension on the Mozilla and Firefox browsers. Analysis of your favorite gene(s) usually require(s) retrieving it from a database like NCBI or Swiss-Prot and then performing one or more tasks including but not limited to:
    • Translation of a nucleotide sequence
    • Blast search (For eg. blastn, blastp etc.) of the desired nucleotide/protein sequence.
    • Calculation of properties (like PI, charge, molecular weight, AT/GC content etc.) of a protein/nucleotide sequence.
    • Conversion between formats (Genbank, Fasta, Swiss-Prot etc.)
    • Prediction of sequence for sub-cellular localization (PREDOTAR, TargetP, pSORT etc.)
    Each of these tasks requires at least the following 4 steps:
    • Visiting one of the sequence database websites,
    • searching for the gene using its name or accession ID (ACC ID),
    • copying the gene sequence
    • and importing it to other bioinformatics websites for further analysis.
    Code bioFOX upon implementation would make analysis of desired sequences easier than it is today. For example, selecting a sequence and submitting it directly to a particular website of interest.

    References:
    1. http://schematron.unl.edu/biofox/
    2. http://biobar.mozdev.org

    Thanks to Yevgeny Ioffe for the tip.

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