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ViennaRNA Package 2.0
New features include an expanded repertoire of tools to assess RNA-RNA interactions and restricted ensembles of structures, additional output information such as centroid structures and maximum expected accuracy structures derived from base pairing probabilities, or z-scores for locally stable secondary structures, and support for input in fasta format.
Fast folding and comparison of RNA secondary structures
- I. Hofacker, W. Fontana, P. Stadler, L. S. Bonhoeffer, M. Tacker, P. Schuster
- Chemistry, Computer Science
- 1 February 1994
SummaryComputer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of…
MITOS: improved de novo metazoan mitochondrial genome annotation.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
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 are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Proteinortho: Detection of (Co-)orthologs in large-scale analysis
- Marcus Lechner, Sven Findeiß, Lydia Steiner, M. Marz, P. Stadler, Sonja J. Prohaska
- BiologyBMC Bioinformatics
- 28 April 2011
Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.
Fast and reliable prediction of noncoding RNAs
All of the known noncoding RNAs and cis-acting elements with high significance are recovered and compelling evidence for many other conserved RNA secondary structures not described so far to the authors' knowledge is found.
Secondary structure prediction for aligned RNA sequences.
The primary transcriptome of the major human pathogen Helicobacter pylori
A novel differential approach selective for the 5′ end of primary transcripts is presented, establishing a paradigm for mapping and annotating the primary transcriptomes of many living species and discovering hundreds of transcriptional start sites within operons, and opposite to annotated genes.
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes and support a highly interleaved organization of the human transcriptome.
RNAalifold: improved consensus structure prediction for RNA alignments
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.