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The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides a web interface to the most commonly used programs of the Vienna RNA package. Among them, we find folding of single and aligned sequences, prediction of RNA-RNA interactions, and design of sequences with a given structure.(More)
The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a set of aligned sequences, is one of the oldest and most widely used tools for this task. In recent years, several alternative approaches have been(More)
RNAz is a widely used software package for de novo detection of structured noncoding RNAs in comparative genomics data. Four years of experience have not only demonstrated the applicability of the approach, but also helped us to identify limitations of the current implementation. RNAz 2.0 provides significant improvements in two respects: (1) The accuracy(More)
BACKGROUND AND PURPOSE FD technology enables reconstructive repair of otherwise difficult-to-treat intracranial aneurysms. These stentlike devices may induce progressive aneurysm thrombosis without additional implants and may initiate complete reverse vessel remodeling. The associated vascular biologic processes are as yet only partially understood. (More)
Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack characteristic signals in primary sequence, comparative(More)
Many non-coding RNA genes and cis-acting regulatory elements of mRNAs contain RNA secondary structures that are critical for their function. Such functional RNAs can be predicted on the basis of thermodynamic stability and evolutionary conservation. We present a web server that uses the RNAz algorithm to detect functional RNA structures in multiple(More)
Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we performed transcriptome-wide mapping of both binding sites of 3' end processing factors CPSF-160,(More)
OBJECTIVE To evaluate whether the objectives of surgical treatment, i.e., prevention of aneurysmal rebleeding, relief of aneurysmal mass effect, and prevention of embolic complications, are met by endosaccular coiling treatment applied to giant and very large wide-necked aneurysms. METHODS Thirty patients with 31 giant or very large aneurysms were(More)
The optimal treatment of spinal dural arteriovenous fistulae (SDAVF) remains controversial and long-term follow-up data, especially data from multidisciplinary treatment, are rarely available. Thus, long-term outcomes following a multidisciplinary approach to the treatment of SDAVF were investigated. The investigation included 26 patients with SDAVF treated(More)
Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential. We systematically assessed the ability of various(More)