Systematic evaluation of spliced alignment programs for RNA-seq data

High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment

BACKGROUND: This study analyzes the predictions of a number of promoter predictors on the ENCODE regions of the human genome as part of the ENCODE Genome Annotation Assessment Project (EGASP). The systems analyzed operate on various principles and we assessed the effectiveness of different conceptual strategies used to correlate produced promoter predictions with the manually annotated 5' gene ends. RESULTS: The predictions were assessed relative to the manual HAVANA annotation of the 5' gene ends. These 5' gene ends were used as the estimated reference transcription start sites. With the maximum allowed distance for predictions of 1,000 nucleotides from the reference transcription start sites, the sensitivity of predictors was in the range 32% to 56%, while the positive predictive value was in the range 79% to 93%. The average distance mismatch of predictions from the reference transcription start sites was in the range 259 to 305 nucleotides. At the same time, using transcription start site estimates from DBTSS and H-Invitational databases as promoter predictions, we obtained a sensitivity of 58%, a positive predictive value of 92%, and an average distance from the annotated transcription start sites of 117 nucleotides. In this experiment, the best performing promoter predictors were those that combined promoter prediction with gene prediction. The main reason for this is the reduced promoter search space that resulted in smaller numbers of false positive predictions. CONCLUSION: The main finding, now supported by comprehensive data, is that the accuracy of human promoter predictors for high-throughput annotation purposes can be significantly improved if promoter prediction is combined with gene prediction. Based on the lessons learned in this experiment, we propose a framework for the preparation of the next similar promoter prediction assessment

Quantum state merging and negative information

We consider a quantum state shared between many distant locations, and define a quantum information processing primitive, state merging, that optimally merges the state into one location. As announced in [Horodecki, Oppenheim, Winter, Nature 436, 673 (2005)], the optimal entanglement cost of this task is the conditional entropy if classical communication is free. Since this quantity can be negative, and the state merging rate measures partial quantum information, we find that quantum information can be negative. The classical communication rate also has a minimum rate: a certain quantum mutual information. State merging enabled one to solve a number of open problems: distributed quantum data compression, quantum coding with side information at the decoder and sender, multi-party entanglement of assistance, and the capacity of the quantum multiple access channel. It also provides an operational proof of strong subadditivity. Here, we give precise definitions and prove these results rigorously.Comment: 23 pages, 3 figure

Tema Con Variazioni: Quantum Channel Capacity

Channel capacity describes the size of the nearly ideal channels, which can be obtained from many uses of a given channel, using an optimal error correcting code. In this paper we collect and compare minor and major variations in the mathematically precise statements of this idea which have been put forward in the literature. We show that all the variations considered lead to equivalent capacity definitions. In particular, it makes no difference whether one requires mean or maximal errors to go to zero, and it makes no difference whether errors are required to vanish for any sequence of block sizes compatible with the rate, or only for one infinite sequence.Comment: 32 pages, uses iopart.cl

Efficient and feasible state tomography of quantum many-body systems

We present a novel method to perform quantum state tomography for many-particle systems which are particularly suitable for estimating states in lattice systems such as of ultra-cold atoms in optical lattices. We show that the need for measuring a tomographically complete set of observables can be overcome by letting the state evolve under some suitably chosen random circuits followed by the measurement of a single observable. We generalize known results about the approximation of unitary 2-designs, i.e., certain classes of random unitary matrices, by random quantum circuits and connect our findings to the theory of quantum compressed sensing. We show that for ultra-cold atoms in optical lattices established techniques like optical super-lattices, laser speckles, and time-of-flight measurements are sufficient to perform fully certified, assumption-free tomography. Combining our approach with tensor network methods - in particular the theory of matrix-product states - we identify situations where the effort of reconstruction is even constant in the number of lattice sites, allowing in principle to perform tomography on large-scale systems readily available in present experiments.Comment: 10 pages, 3 figures, minor corrections, discussion added, emphasizing that no single-site addressing is needed at any stage of the scheme when implemented in optical lattice system

Entanglement and localization of wavefunctions

We review recent works that relate entanglement of random vectors to their localization properties. In particular, the linear entropy is related by a simple expression to the inverse participation ratio, while next orders of the entropy of entanglement contain information about e.g. the multifractal exponents. Numerical simulations show that these results can account for the entanglement present in wavefunctions of physical systems.Comment: 6 pages, 4 figures, to appear in the proceedings of the NATO Advanced Research Workshop 'Recent Advances in Nonlinear Dynamics and Complex System Physics', Tashkent, Uzbekistan, 200