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Register a new userAnalytical Study of Hexapod miRNAs using Phylogenetic Methods
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MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene expression. Identification of total number of miRNAs even in completely sequenced organisms is still an open problem. However, researchers have been using techniques that can predict limited number of miRNA in an organism. In this paper, we have used homology based approach for comparative analysis of miRNA of hexapoda group .We have used Apis mellifera, Bombyx mori, Anopholes gambiae and Drosophila melanogaster miRNA datasets from miRBase repository. We have done pair wise as well as multiple alignments for the available miRNAs in the repository to identify and analyse conserved regions among related species. Unfortunately, to the best of our knowledge, miRNA related literature does not provide in depth analysis of hexapods. We have made an attempt to derive the commonality among the miRNAs and to identify the conserved regions which are still not available in miRNA repositories. The results are good approximation with a small number of mismatches. However, they are encouraging and may facilitate miRNA biogenesis for
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Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However, the nonlinear transcript structures and the ultra-high throughput of RNA-Seq reads pose significant algorithmic and computational challenges to the existing transcriptome assembly approaches, either reference-guided or de novo. While reference-guided approaches offer good sensitivity, they rely on alignment results of the splice-aware aligners and are thus unsuitable for species with incomplete reference genomes. In contrast, de novo approaches do not depend on the reference genome but face a computational daunting task derived from the complexity of the graph built for the whole transcriptome. In response to these challenges, we present a hybrid approach to exploit an incomplete reference genome without relying on splice-aware aligners. We have designed a split-and-align procedure to efficiently localize the reads to individual genomic loci, which is followed by an accurate de novo assembly to assemble reads falling into each locus. Using extensive simulation data, we demonstrate a high accuracy and precision in transcriptome reconstruction by comparing to selected transcriptome assembly tools. Our method is implemented in assemblySAM, a GUI software freely available at http://sammate.sourceforge.net.
Motivation: Optimizing seed selection is an important problem in read mapping. The number of non-overlapping seeds a mapper selects determines the sensitivity of the mapper while the total frequency of all selected seeds determines the speed of the mapper. Modern seed-and-extend mappers usually select seeds with either an equal and fixed-length scheme or with an inflexible placement scheme, both of which limit the potential of the mapper to select less frequent seeds to speed up the mapping process. Therefore, it is crucial to develop a new algorithm that can adjust both the individual seed length and the seed placement, as well as derive less frequent seeds. Results: We present the Optimal Seed Solver (OSS), a dynamic programming algorithm that discovers the least frequently-occurring set of x seeds in an L-bp read in $O(x times L)$ operations on average and in $O(x times L^{2})$ operations in the worst case. We compared OSS against four state-of-the-art seed selection schemes and observed that OSS provides a 3-fold reduction of average seed frequency over the best previous seed selection optimizations.
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their chloroplasts, the phylogenetic tree that can be inferred by their core genes is not necessarily well supported, due to the possible occurrence of problematic genes (i.e., homoplasy, incomplete lineage sorting, horizontal gene transfers, etc.) which may blur the phylogenetic signal. However, a trustworthy phylogenetic tree can still be obtained provided such a number of blurring genes is reduced. The problem is thus to determine the largest subset of core genes that produces the best-supported tree. To discard problematic genes and due to the overwhelming number of possible combinations, this article focuses on how to extract the largest subset of sequences in order to obtain the most supported species tree. Due to computational complexity, a distributed Binary Particle Swarm Optimization (BPSO) is proposed in sequential and distributed fashions. Obtained results from bo
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation but also the higher level organization of the cell. With the advent of high-throughput techniques in molecular biology, significant amount of physical interaction data has been cataloged from organisms such as yeast, which has in turn fueled computational approaches to systematically mine complexes from the network of physical interactions among proteins (PPI network). In this survey, we review, classify and evaluate some of the key computational methods developed till date for the identification of protein complexes from PPI networks. We present two insightful taxonomies that reflect how these methods have evolved over the years towards improving automated complex prediction. We also discuss some open challenges facing accurate reconstruction of complexes, the crucial ones being presence of high proportion of errors and noise in current high-throughput datasets and some key aspects overlooked by current complex detection methods. We hope this review will not only help to condense the history of computational complex detection for easy reference, but also provide valuable insights to drive further research in this area.
Managing the prediction of metrics in high-frequency financial markets is a challenging task. An efficient way is by monitoring the dynamics of a limit order book to identify the information edge. This paper describes the first publicly available benchmark dataset of high-frequency limit order markets for mid-price prediction. We extracted normalized data representations of time series data for five stocks from the NASDAQ Nordic stock market for a time period of ten consecutive days, leading to a dataset of ~4,000,000 time series samples in total. A day-based anchored cross-validation experimental protocol is also provided that can be used as a benchmark for comparing the performance of state-of-the-art methodologies. Performance of baseline approaches are also provided to facilitate experimental comparisons. We expect that such a large-scale dataset can serve as a testbed for devising novel solutions of expert systems for high-frequency limit order book data analysis.
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