MOTIVATION: Small nucleolar RNAs (snoRNAs) are an abundant class of non-coding RNAs with a wide variety of cellular functions including chemical modification of RNA, telomere maintanance, pre-rRNA processing and regulatory activities in alternative splicing. The main role of box C/D snoRNAs is to determine the targets for 2'-O-ribose methylation, which is important for rRNA maturation and splicing regulation of some mRNAs. The targets are still unknown, however, for many 'orphan' snoRNAs. While a fast and efficient target predictor for box H/ACA snoRNAs is available, no comparable tool exists for box C/D snoRNAs, even though they bind to their targets in a much less complex manner. RESULTS: PLEXY is a dynamic programming algorithm that computes thermodynamically optimal interactions of a box C/D snoRNA with a putative target RNA. Implemented as scanner for large input sequences and equipped with filters on the duplex structure, PLEXY is an efficient and reliable tool for the prediction of box C/D snoRNA target sites. AVAILABILITY: The perl script PLEXY is freely available at http://www.bioinf.uni-leipzig.de/Software/PLEXY.
MOTIVATION: Small nucleolar RNAs (snoRNAs) are an abundant class of non-coding RNAs with a wide variety of cellular functions including chemical modification of RNA, telomere maintanance, pre-rRNA processing and regulatory activities in alternative splicing. The main role of box C/D snoRNAs is to determine the targets for 2'-O-ribose methylation, which is important for rRNA maturation and splicing regulation of some mRNAs. The targets are still unknown, however, for many 'orphan' snoRNAs. While a fast and efficient target predictor for box H/ACA snoRNAs is available, no comparable tool exists for box C/D snoRNAs, even though they bind to their targets in a much less complex manner. RESULTS: PLEXY is a dynamic programming algorithm that computes thermodynamically optimal interactions of a box C/D snoRNA with a putative target RNA. Implemented as scanner for large input sequences and equipped with filters on the duplex structure, PLEXY is an efficient and reliable tool for the prediction of box C/D snoRNA target sites. AVAILABILITY: The perl script PLEXY is freely available at http://www.bioinf.uni-leipzig.de/Software/PLEXY.
Authors: Manja Marz; Andreas R Gruber; Christian Höner Zu Siederdissen; Fabian Amman; Stefan Badelt; Sebastian Bartschat; Stephan H Bernhart; Wolfgang Beyer; Stephanie Kehr; Ronny Lorenz; Andrea Tanzer; Dilmurat Yusuf; Hakim Tafer; Ivo L Hofacker; Peter F Stadler Journal: RNA Biol Date: 2011-11-01 Impact factor: 4.652
Authors: Jiyeon Lee; Alexis N Harris; Christopher L Holley; Jana Mahadevan; Kelly D Pyles; Zeno Lavagnino; David E Scherrer; Hideji Fujiwara; Rohini Sidhu; Jessie Zhang; Stanley Ching-Cheng Huang; David W Piston; Maria S Remedi; Fumihiko Urano; Daniel S Ory; Jean E Schaffer Journal: J Clin Invest Date: 2016-11-07 Impact factor: 14.808
Authors: Hadi Jorjani; Stephanie Kehr; Dominik J Jedlinski; Rafal Gumienny; Jana Hertel; Peter F Stadler; Mihaela Zavolan; Andreas R Gruber Journal: Nucleic Acids Res Date: 2016-05-12 Impact factor: 16.971