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.
- First, pairs of individual read blocks are compared using a modified
Smith-Waterman alignment algorithm.
- Second, block groups are compared by means of a scoring function that
evaluates both the similarity of the individual blocks and the pattern of distances within
the block groups. For this purpose a modified sankoff algorithm is used.
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)