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We investigate usage of dynamic time warping (DTW) algorithm for aligning raw signal data from MinION sequencer. DTW is mostly using for fast alignment for selective sequencing to quickly determine whether a read comes from sequence of interest. We show that standard usage of DTW has low discriminative power mainly due to problem with accurate estimation of scaling parameters. We propose a simple variation of DTW algorithm, which does not suffer from scaling problems and has much higher discriminative power.
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we show that th
In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when the NGS read
RNA-seq has rapidly become the de facto technique to measure gene expression. However, the time required for analysis has not kept up with the pace of data generation. Here we introduce Sailfish, a novel computational method for quantifying the abund
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several
We propose a simple tractable pair hidden Markov model for pairwise sequence alignment that accounts for the presence of short tandem repeats. Using the framework of gain functions, we design several optimization criteria for decoding this model and