Communications of the ACM
CM Software Assembles Rna Transcripts More Accurately
Carnegie Mellon University researchers have developed a program that is a more accurate computational method for reconstructing full-length nucleotide sequences of the RNA products in cells.
Credit: KhanAcademy.org
Researchers at Carnegie Mellon University's Computational Biology Department have developed Scallop, a program that is a more accurate computational method for reconstructing full-length nucleotide sequences of the RNA products in cells.
Scallop will help scientists build a more complete library of RNA transcripts and help them better understand the regulation of gene expression.
The software is a transcript assembler, meaning it takes fragments of RNA sequences, called reads, that are produced by high-throughput RNA sequencing technologies, and reassembling them to reconstruct complete RNA transcripts.
The researchers say Scallop is 34.5% to 36.6% more accurate than the two other leading assemblers for transcripts consisting of multiple exons.
Scallop functions by constructing a graph to organize reads that are mapped to the corresponding locations on the gene's DNA. The program uses a novel algorithm to take advantage of the information from reads that span several exons to guide it to the correct assembly paths.
From CMU Computational Biology Department
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