Figure S1 - Knowledge-Based Reconstruction of mRNA Transcripts with Short Sequencing Reads for Transcriptome Research

A reconstruction example of TPM2. Our proposed algorithm was compared with the Cufflink reference annotation based transcript (RABT) assembly algorithm [Robert et al, Bioinformatics, 2011] over a simplified example of TPM2 gene. Given two reference transcripts of the gene (Ref1 and 2), sequencing reads tiling across a new exon (highlighted) and its connected exons were fed into each algorithm. The Cufflink RABT was able to assemble only one new transcript where the new exon is assembled with one of the two reference isoforms of the gene (CUFF.2.2) while our proposed algorithm generated two new transcripts with the new exon integrated to each of the two reference isoforms (JucWalk 1 and 2). (EPS)