TruHMM: an algorithm for assembling full-length transcripts in prokaryotes using directional RNA-Seq short reads

Although RNA-seq has become the major method for analyzing the complexity of prokaryotic transcriptome, it is still a challenging task to accurately assemble full length transcripts using short RNA-seq reads.

Researchers from the University of North Carolina at Charlotte have profiled the transcriptomes of E. coli K12 under different culture conditions and growth phases using a highly specific directional RNA-seq technique that can capture various types of transcripts in the bacterial cells, combined with a highly accurate and robust algorithm and tool TruHMM for assembling full length transcripts. They found that 46.9 ~ 63.4% of expressed operons were utilized in their putative alternative forms, 72.23 ~ 89.54% genes had putative asRNA transcripts and 51.37 ~ 72.74% intergenic regions had putative ncRNA transcripts under different culture conditions and growth phases.

rna-seqAs has been demonstrated in many other prokaryotes, E. coli K12 also has a highly complex and dynamic transcriptomes under different culture conditions and growth phases. Such complex and dynamic transcriptomes might play important roles in the physiology of the bacterium. TruHMM is a highly accurate and robust algorithm for assembling full-length transcripts in prokaryotes using directional RNA-seq short reads.

Availability – TruHMM is available at http://bioinfolab.uncc.edu/TruHmm_package/

  • Li S, Dong X, Su Z. (2013) Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling. BMC Genomics 14(1), 520. [abstract]