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ViennaRNA Package 2.0
TLDR
The ViennaRNA Package 2.0 now implements the latest energy model, provides many new and improved functionalities, and - as we hope - is even easier and more efficient to use due to a thread-safe architecture, an improved API, a more consistent set of options. Expand
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Fast folding and comparison of RNA secondary structures
TLDR
An efficient heuristic for the inverse folding problem of RNA is introduced. Expand
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These dataExpand
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Fast and reliable prediction of noncoding RNAs
We report an efficient method for detecting functional RNAs. The approach, which combines comparative sequence analysis and structure prediction, already has yielded excellent results for a smallExpand
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MITOS: improved de novo metazoan mitochondrial genome annotation.
About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. ThisExpand
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The primary transcriptome of the major human pathogen Helicobacter pylori
TLDR
Using a novel differential approach (dRNA-seq) selective for the 5′ end of primary transcripts, we present a genome-wide map of H. pylori transcriptional start sites and operons. Expand
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Proteinortho: Detection of (Co-)orthologs in large-scale analysis
TLDR
We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. Expand
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RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the associations of human nuclear andExpand
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Secondary structure prediction for aligned RNA sequences.
Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNAExpand
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RNAalifold: improved consensus structure prediction for RNA alignments
TLDR
We show that the accuracy of RNAalifold predictions can be improved substantially by introducing a different, more rational handling of alignment gaps, and by replacing the rather simplistic model of covariance scoring with more sophisticated RIBOSUM-like scoring matrices. Expand
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