Transcript mapping based on dRNA-seq data.
BACKGROUND
RNA-seq and its variant differential RNA-seq (dRNA-seq) are today routine methods for transcriptome analysis in bacteria. While expression profiling and transcriptional start site prediction are standard tasks today, the problem of identifying transcriptional units in a genome-wide fashion is still not solved for prokaryotic systems.


RESULTS
We present RNAseg, an algorithm for the prediction of transcriptional units based on dRNA-seq data. A key feature of the algorithm is that, based on the data, it distinguishes between transcribed and un-transcribed genomic segments. Furthermore, the program provides many different predictions in a single run, which can be used to infer the significance of transcriptional units in a consensus procedure. We show the performance of our method based on a well-studied dRNA-seq data set for Helicobacter pylori.


CONCLUSIONS
With our algorithm it is possible to identify operons and 5'- and 3'-UTRs in an automated fashion. This alleviates the need for labour intensive manual inspection and enables large-scale studies in the area of comparative transcriptomics.
Thorsten
T
Bischler
Matthias
M
Kopf
Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr, 1, 79104 Freiburg, Germany. bjoern.voss@biologie.uni-freiburg.de.
Björn
B
Voß
D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics; D016480:Helicobacter pylori / Q000235:genetics; D009876:Operon; D017423:Sequence Analysis, RNA / Q000379:methods*; D024363:Transcription Initiation Site; D020506:Untranslated Regions
D020506:Untranslated Regions