Abstract:The background-weighted histogram (BWH) algorithm proposed in [2] attempts to reduce the interference of background in target localization in mean shift tracking. However, in this paper we prove that the weights assigned to pixels in the target candidate region by BWH are proportional to those without background information, i.e. BWH does not introduce any new information because the mean shift iteration formula is invariant to the scale transformation of weights. We then propose a corrected BWH (CBWH) formula by transforming only the target model but not the target candidate model. The CBWH scheme can effectively reduce background's interference in target localization. The experimental results show that CBWH can lead to faster convergence and more accurate localization than the usual target representation in mean shift tracking. Even if the target is not well initialized, the proposed algorithm can still robustly track the object, which is hard to achieve by the conventional target representation.
MotivationTranslation initiation is a key step in the regulation of gene expression. In addition to the annotated translation initiation sites (TISs), the translation process may also start at multiple alternative TISs (including both AUG and non-AUG codons), which makes it challenging to predict TISs and study the underlying regulatory mechanisms. Meanwhile, the advent of several high-throughput sequencing techniques for profiling initiating ribosomes at single-nucleotide resolution, e.g. GTI-seq and QTI-seq, provides abundant data for systematically studying the general principles of translation initiation and the development of computational method for TIS identification.MethodsWe have developed a deep learning-based framework, named TITER, for accurately predicting TISs on a genome-wide scale based on QTI-seq data. TITER extracts the sequence features of translation initiation from the surrounding sequence contexts of TISs using a hybrid neural network and further integrates the prior preference of TIS codon composition into a unified prediction framework.ResultsExtensive tests demonstrated that TITER can greatly outperform the state-of-the-art prediction methods in identifying TISs. In addition, TITER was able to identify important sequence signatures for individual types of TIS codons, including a Kozak-sequence-like motif for AUG start codon. Furthermore, the TITER prediction score can be related to the strength of translation initiation in various biological scenarios, including the repressive effect of the upstream open reading frames on gene expression and the mutational effects influencing translation initiation efficiency.Availability and ImplementationTITER is available as an open-source software and can be downloaded from https://github.com/zhangsaithu/titer.Supplementary information
Supplementary data are available at Bioinformatics online.
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