PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
Name
Lin-2011-PhyloCSF.pdf
Size
1.08 MB
Format
Adobe PDF
Checksum (MD5)
e6b01f860a73b6e2c0aecde4dd7e34e9
Author(s)
Lin, Michael F.
Jungreis, Irwin
Kellis, Manolis
Date Issued
July 2011
Journal
Bioinformatics
Publisher
Oxford University Press
Citation
Lin, Michael F., Irwin Jungreis, and Manolis Kellis. “PhyloCSF: a Comparative Genomics Method to Distinguish Protein Coding and Non-coding Regions.” Bioinformatics 27.13 (2011): i275–i282. Web.
Version
Final published version
Abstract
Motivation: As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multispecies nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models.
Results: We show that PhyloCSF's classification performance in 12-species Drosophila genome alignments exceeds all other methods we compared in a previous study. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE, and as interest grows in long non-coding RNAs, often initially recognized by their lack of protein coding potential rather than conserved RNA secondary structures.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Terms of Use
Creative Commons Attribution Non-Commercial
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1093/bioinformatics/btr209
