PMID- 28334186
OWN - NLM
STAT- Publisher
DA  - 20170323
LR  - 20170323
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Linking)
DP  - 2017 Feb 27
TI  - RNAscClust: clustering RNA sequences using structure conservation and graph based
      motifs.
LID - 10.1093/bioinformatics/btx114 [doi]
AB  - Motivation: Clustering RNA sequences with common secondary structure is an
      essential step towards studying RNA function. Whereas structural RNA alignment
      strategies typically identify common structure for orthologous structured RNAs,
      clustering seeks to group paralogous RNAs based on structural similarities.
      However, existing approaches for clustering paralogous RNAs, do not take the
      compensatory base pair changes obtained from structure conservation in
      orthologous sequences into account. Results: Here, we present RNAscClust, the
      implementation of a new algorithm to cluster a set of structured RNAs taking
      their respective structural conservation into account. For a set of multiple
      structural alignments of RNA sequences, each containing a paralog sequence
      included in a structural alignment of its orthologs, RNAscClust computes minimum 
      free-energy structures for each sequence using conserved base pairs as prior
      information for the folding. The paralogs are then clustered using a graph
      kernel-based strategy, which identifies common structural features.We show that
      the clustering accuracy clearly benefits from an increasing degree of
      compensatory base pair changes in the alignments. Availability: RNAscClust is
      available at http://www.bioinf.uni-freiburg.de/Software/RNAscClust. Contact:
      gorodkin@rth.dk or backofen@informatik.uni-freiburg.de. Supplementary
      information: Supplementary data are available at Bioinformatics online.
FAU - Miladi, Milad
AU  - Miladi M
AD  - Bioinformatics Group, Department of Computer Science, University of Freiburg,
      Germany.
FAU - Junge, Alexander
AU  - Junge A
AD  - Center for non-coding RNA in Technology and Health, University of Copenhagen,
      Denmark.
AD  - Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, 
      Denmark.
FAU - Costa, Fabrizio
AU  - Costa F
AD  - Bioinformatics Group, Department of Computer Science, University of Freiburg,
      Germany.
FAU - Seemann, Stefan E
AU  - Seemann SE
AD  - Center for non-coding RNA in Technology and Health, University of Copenhagen,
      Denmark.
AD  - Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, 
      Denmark.
FAU - Hull Havgaard, Jakob
AU  - Hull Havgaard J
AD  - Center for non-coding RNA in Technology and Health, University of Copenhagen,
      Denmark.
AD  - Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, 
      Denmark.
FAU - Gorodkin, Jan
AU  - Gorodkin J
AD  - Center for non-coding RNA in Technology and Health, University of Copenhagen,
      Denmark.
AD  - Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, 
      Denmark.
FAU - Backofen, Rolf
AU  - Backofen R
AD  - Bioinformatics Group, Department of Computer Science, University of Freiburg,
      Germany.
AD  - Center for non-coding RNA in Technology and Health, University of Copenhagen,
      Denmark.
AD  - Center for Biological Signalling Studies (BIOSS), University of Freiburg,
      Germany.
LA  - eng
PT  - Journal Article
DEP - 20170227
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
EDAT- 2017/03/24 06:00
MHDA- 2017/03/24 06:00
CRDT- 2017/03/24 06:00
PHST- 2016/06/06 [received]
PHST- 2017/02/21 [accepted]
AID - 3056002 [pii]
AID - 10.1093/bioinformatics/btx114 [doi]
PST - aheadofprint
SO  - Bioinformatics. 2017 Feb 27. doi: 10.1093/bioinformatics/btx114.