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The bioinformatics tools were executed for analyzing the sequences of soybean SNP sites and selecting the appropriate restriction endonucleases.
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The standalone versions of several bioinformatics tools were locally installed and executed to generate annotations for soybean transcription factors.
Each tool was executed 100 times per constraint set, to enable statistics.
Bioinformatics tools were used for data evaluation.
Bioinformatics tools were recently developed to distinguish between driver and passenger nsSNPs [68], [69].
Information about bioinformatics tools was obtained by downloading the titles and abstracts of articles published since 2010 in four leading journals in the field of bioinformatics: BMC Bioinformatics, Bioinformatics, Database, and Nucleic Acids Research.
Different bioinformatics tools are likely to produce different results.
All the following bioinformatics analyses were executed on PS genes lists obtained as described above.
The QOL measurements were executed using validated measurement tools.
Gene interaction analyses were executed using Ingenuity Pathways Analysis (IPA) tools 3.0 http://www.ingenuity.com.com
The K-means clustering were executed in MATLAB, using both the Bioinformatics and Statistics toolboxes.
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