Figure 2
From: Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study
Steps of lncRScan. (1) ‘extract_category’ extracts five candidate categories of assemblies (Transcripts-1), including ‘i’, ‘j’, ‘o’, ‘u’ and ‘x’; (2) ‘extract_length’ is used to extract the transcripts with length > 200 nt (Transcripts-2); (3) ‘extract_ORF’ selects the transcripts with maximum putative ORF < 300 nt (Transcripts-3); (4) ‘extract_PhyloCSF’ extracts the transcripts with PhyloCSF score < 0 or test failure due to ORF < 25 aa (Transcripts-4); (5) ’extract_Pfam’ searches the remaining transcripts in the Pfam database and excludes the transcripts with significant protein domain hits. Towards the end of lncRScan, the remaining 308 transcripts (Transcripts-5) are defined as the novel lncRNAs.