JANE allows in particular assembly of large-scale RNA data on prokaryotic genomes even if the genome sequence is not known (it then can use any related genome as a template, as the transriptome project continues, the genome sequence is calculated. Furthermore, different RNAs are mapped, annotated and compared. The software is also useful for single cell sequencing (DNA level) and assemblies.
Users could upload sequence reads and reference genome, then perform a detailed mapping job at JANE workbench: http://jane.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/inputest.pl
Prof. Dandekar (firstname.lastname@example.org)