TOA-Manuscript-Performance-Evaluation-Tests

<p><strong>Table of contents</strong></p> <p>This repository contains the data that support the findings of the manuscript</p> <p>&quot;TOA: a software package for automated functional annotation in non-model plant species&quot;.</p> <p><strong>Directories:</strong></p> <p><strong>BenchmarkTranscriptomes:</strong> Fasta files with the sequences corresponding to the benchmark transcriptomes tested in the manuscript:</p> <p><strong>Cnuc:</strong> <em>Cocos nucifera</em> embryos (Huang et al., 2014).</p> <p><strong>Fsyl:</strong> <em>Fagus sylvatica</em> leaves (M&uuml;ller, Seifert, L&uuml;bbe, Leuschner, &amp; Finkeldey, 2017).</p> <p><strong>Pcan:</strong> <em>Pinus canariensis</em> immature xylem (Chano, Collada, &amp; Soto, 2017).</p> <p><strong>GoldStandardTranscripts:</strong> transcripts fasta files of two well known gene families of proteins in <em>Arabidopsis thaliana</em> fetched from TAIR: the kinesins gene family (GS1) (Reddy &amp; Day, 2001) and the monolignol biosynthesis gene family (GS2) (Raes et al., 2003)</p> <p><strong>EnTAP:</strong> output of the six simulation tests performed with EnTAP.</p> <p><strong>TOA:</strong> output of the six simulation tests performed with TOA.</p> <p><strong>TRAPID:</strong> output of the three simulation tests performed with TRAPID.</p> <p><strong>Trinotate:</strong> output of the three simulation tests performed with Trinotate.</p> <p><br> &nbsp;</p> <p><strong>References:</strong></p> <p>Chano, V., Collada, C., &amp; Soto, A. (2017). Transcriptomic analysis of wound xylem formation in <em>Pinus canariensis</em>. <em>BMC Plant Biology</em>, <em>17</em>(234). doi:10.1186/s12870-017-1183-3</p> <p>Huang, Y. Y., Lee, C. P., Fu, J. L., Chang, B. C. H., Matzke, A. J. M., &amp; Matzke, M. (2014). <em>De novo</em> transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation. <em>G3: Genes, Genomes, Genetics</em>, <em>4</em>(11), 2147&ndash;2157. doi:10.1534/g3.114.013409</p> <p>M&uuml;ller, M., Seifert, S., L&uuml;bbe, T., Leuschner, C., &amp; Finkeldey, R. (2017). <em>De novo</em> transcriptome assembly and analysis of differential gene expression in response to drought in European beech. <em>PLoS ONE</em>, <em>12</em>(9), 1&ndash;20. doi:10.1371/journal.pone.0184167</p> <p><br> &nbsp;</p> <p><br> &nbsp;</p>