Supplementary Supplementary Supplementary Supplementary Methods Methods Methods Methods Comparison Comparison Comparison Comparison of of of of Cnci Cnci Cnci Cnci Performance Performance Performance Performance with with with with Cpc Cpc Cpc Cpc and and
Supplementary Supplementary Supplementary Supplementary Methods Methods Methods Methods Comparison Comparison Comparison Comparison of of of of Cnci Cnci Cnci Cnci Performance Performance Performance Performance with with with with Cpc Cpc Cpc Cpc and and
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教程，这将使用户能够重现我们在这项工作中提出的分析类型。为了将CNCI的性能与其他方法进行比较，我们使用CPC和CMCSF重新分析了测试集。为了运行CPC分析，我们将测试成绩单直接以Fasta格式提交到CPC的网站，并使用默认参数，并返回了一系列明确的结果，这些结果在质量评分之后标记有蛋白质编码和非编码。为了进行BSCSF分析，我们将BED格式的测试转录本上传到Galaxy，Galaxy通过“缝合MAF块“功能将BED文件转换为29个物种的多重比对格式。之后，我们将这些多个比对文件提交给了CRISPCSF（从http：//compbio.mit.edu/PhyloCSF下载），
tutorial that will enable the user to reproduce the type of analysis we present in this work. To compare CNCI performance with other methods, we re-analyzed the testing set using CPC and phyloCSF. To run CPC analyses, we submitted the testing transcripts to CPC's website directly in Fasta format and used default parameters, and a list of definitive results marked with protein-coding and non-coding following the quality score were returned. To perform phyloCSF analyses, we uploaded the testing transcripts in BED format to the Galaxy, which converted the BED file to 29 species multiple alignment format by " stitch MAF blocks " function. After that, we submitted these multiple alignment files to phyloCSF (downloaded from http://compbio.mit.edu/PhyloCSF) with the