Welcome to the deepBlockAlign web page


Many transcripts in cell undergo post-transcriptional processes that generate short RNA sequence fragments. When these fragments are mapped back to the reference genome they often form distinctive patterns that convey information on structure and processing of their parent transcripts. A well known pattern arises is formed e.g. by the miR and miR* reads generated from microRNA precursors.

deepBlockAlign is a tool for the alignment of two RNA-seq read patterns. The analysis starts from closely spaced blocks of mapped reads, which we call block groups or read profiles. The comparison of two block groups is done in two stages.


Langenberger D*, Pundhir S*, Ekstrøm CT, Stadler PF, Hoffmann S and Gorodkin J.(2012) deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinformatics. 28(1):17-24 [PMID: 22053076] (*joint first authors)


sachin@rth.dk, david@bioinfo.uni-leipzig.de