Set Of Candidate Sequences Research Articles

Improved Selected Mapping Technique for Reduction of PAPR in OFDM Systems

High peak to average power ratio (PAPR) is a limiting factor towards the performance of an OFDM system. Selected Mapping (SLM) is a popular peak to average power ratio (PAPR) reduction scheme used with the OFDM systems. In this technique, U set of candidate sequences are generated that leads to improvement in the PAPR reduction ability of the OFDM systems. The major concern of the conventional SLM is that as the number of candidates is increased, there is a proportional rise in the inverse fast Fourier transforms (IFFT) computations of the systems. In our article we have proposed a scheme in which we increase the number of candidate sequence as (U+U2/4) that leads to improved PAPR performance of the OFDM systems without any equivalent rise in the IFFT computations. It has been demonstrated that both the simulation and analytical results are well-approximated in our proposed schemes. We also estimate the threshold value of PAPR at a fixed value of complementary cumulative distribution function (CCDF) for different number of subcarriers and candidate sequences. Results demonstrate that our proposed scheme outperforms in terms of PAPR reduction ability of the OFDM signal and obtains effective PAPR threshold values with negligible loss in BER performance of the system.

Speed Up Similarity Search of Time Series Under Dynamic Time Warping

Similarity search is a foundational task in time series data mining. Although there are many ways to measure the similarity of time series, a lot of evidence indicates that dynamic time warping (DTW) has the best robustness in many applications. Unfortunately, the expensive computational cost limits its application in large-scale databases. To speed up similarity search under DTW, we design a framework of two-stage similarity search for time series. In the first stage, we propose an improved lower bounding distance, which can be used to discard plenty of dissimilar series to get a set of candidate sequences. In the second stage, to efficiently get the retrieval result from the set of candidate sequences, we explore early abandoning strategy to avoid the full calculation of DTW. Extensive experiments are conducted on real-world data sets. The experimental results indicate that the proposed method can improve the retrieval efficiency of similarity search under DTW and guarantee no false dismissals.

BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing

BackgroundCurrent high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them into a mix containing a number of libraries to be sequenced simultaneously. After sequencing, the samples are binned by identifying the barcode sequence within each sequence read.In order to tolerate sequencing errors, barcodes should be sufficiently apart from each other in sequence space. An additional constraint due to both nucleotide usage and basecalling accuracy is that the proportion of different nucleotides should be in balance in each barcode position. The number of samples to be mixed in each sequencing run may vary and this introduces a problem how to select the best subset of available barcodes at sequencing core facility for each sequencing run. There are plenty of tools available for de novo barcode design, but they are not suitable for subset selection.ResultsWe have developed a tool which can be used for three different tasks: 1) selecting an optimal barcode set from a larger set of candidates, 2) checking the compatibility of user-defined set of barcodes, e.g. whether two or more libraries with existing barcodes can be combined in a single sequencing pool, and 3) augmenting an existing set of barcodes.In our approach the selection process is formulated as a minimization problem. We define the cost function and a set of constraints and use integer programming to solve the resulting combinatorial problem. Based on the desired number of barcodes to be selected and the set of candidate sequences given by user, the necessary constraints are automatically generated and the optimal solution can be found. The method is implemented in C programming language and web interface is available at http://ekhidna2.biocenter.helsinki.fi/barcosel.ConclusionsIncreasing capacity of sequencing platforms raises the challenge of mixing barcodes. Our method allows the user to select a given number of barcodes among the larger existing barcode set so that both sequencing errors are tolerated and the nucleotide balance is optimized. The tool is easy to access via web browser.