SNPServer: a real-time SNP discovery tool Savage, David; Batley, Jacqueline; Erwin, Tim ...
Nucleic acids research,
07/2005, Letnik:
33, Številka:
suppl-2
Journal Article
Recenzirano
Odprti dostop
SNPServer is a real-time flexible tool for the discovery of SNPs (single nucleotide polymorphisms) within DNA sequence data. The program uses BLAST, to identify related sequences, and CAP3, to ...cluster and align these sequences. The alignments are parsed to the SNP discovery software autoSNP, a program that detects SNPs and insertion/deletion polymorphisms (indels). Alternatively, lists of related sequences or pre-assembled sequences may be entered for SNP discovery. SNPServer and autoSNP use redundancy to differentiate between candidate SNPs and sequence errors. For each candidate SNP, two measures of confidence are calculated, the redundancy of the polymorphism at a SNP locus and the co-segregation of the candidate SNP with other SNPs in the alignment. SNPServer is available at http://hornbill.cspp.latrobe.edu.au/snpdiscovery.html.
Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research. InterStoreDB is a suite of integrated databases ...designed to assist in this process. The individual databases are species independent and generic in design, providing access to curated datasets relating to plant populations, phenotypic traits, genetic maps, marker loci and QTL, with links to functional gene annotation and genomic sequence data. Each component database provides access to associated metadata, including data provenance and parameters used in analyses, thus providing users with information to evaluate the relative worth of any associations identified. The databases include CropStoreDB, for management of population, genetic map, QTL and trait measurement data, SeqStoreDB for sequence‐related data and AlignStoreDB, which stores sequence alignment information, and allows navigation between genetic and genomic datasets. Genetic maps are visualized and compared using the CMAP tool, and functional annotation from sequenced genomes is provided via an EnsEMBL‐based genome browser. This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal. We demonstrate the value of InterStoreDB as a tool for Brassica research. InterStoreDB is available from: http://www.interstoredb.org
The BASC system provides tools for integrated mining and browsing of genetic, genomic and phenotypic data. The BASC demonstration server provides access to raw and analysed information for Brassica ...species and comparative information with Arabidopsis. We can use the tools within the Brassica BASC server to identify candidate genes for traits, conduct genome comparisons with Arabidopsis, identify syntenic regions and view gene expression profiles. The integration of BASC modules allows researchers to gain a comprehensive view of diverse Brassica genetic, genomic and phenotypic information. This chapter demonstrates the application of this resource, through the identification of candidate genes for an observed seed oil quality trait in Brassica napus.
The increasing adoption of low power wide area networks (LPWANs) for Internet of Things (IoT) devices requires a thorough examination of network dynamics for multi-cell networks. This study ...introduces a novel scheme for multi-cell LPWAN and assesses the success probability for end devices at the cell edge using stochastic geometry to model intra-cell interference. We identify the optimal number of cells for a guaranteed minimum success probability, revealing that small cells enhance the average signal-to-interference-noise ratio. It benefits devices at the cell edge, addressing the challenges posed by the growing number of IoT devices in LPWANs.
Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying ...complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast- and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement.
Abstract
The ascomycete Sclerotinia sclerotiorum is a plant pathogen with a very broad host range. In order to identify and characterize genes involved in S. sclerotiorum infection of Brassica napus ...(canola), expressed sequence tags (ESTs) were examined from libraries prepared from three tissues: complex appressorium (infection cushions), mycelia grown on agar and lesions formed on leaves of B. napus. A high proportion of genes (68%) had not been previously reported for S. sclerotiorum in public gene or EST databases. The types of novel genes identified in the infection cushion library highlights the functional specificity of these structures and similarities to appressoria in other fungal pathogens. Quantitative real-time PCR was used to analyse tissue specificity and timing of transcription of genes with best matches to MAS3 (appressoria-associated protein from Magnaporthe grisea), cellobiohydrolase I, oxaloacetate acetylhydrolase, metallothionein, pisatin demethylase, and an unknown gene with orthologs in fungal pathogens but not in saprophytic fungi.
Opportunistic spectrum access is a viable technique for cognitive radio (CR) networks to address the spectrum scarcity problem, where both spectrum sensing and resource allocation (SSRA) are ...significant to the system throughput performance. Previous works on SSRA often require complete network statistics which may not be feasible given the time-varying nature of practical CR networks. In this paper, we propose a learning-based optimization framework for SSRA in multi-band-multi-user CR networks. We develop a dynamic cooperative spectrum sensing strategy which allows secondary users to detect available spectrum bands of the primary user, followed by flexible power allocation for efficient data transmissions. To cope with the dynamic of channel and resource statistics, we propose an improved deep reinforcement learning scheme based on a maximum entropy-enabled actor critic algorithm. Numerical results demonstrate the superiority of our approach over existing schemes.
In order to better assess the ecological importance of offshore petroleum platforms for economically important groundfishes, we quantified the degree of site fidelity of 100 platform-associated ...individuals representing 15 species at three offshore platforms in the Santa Barbara Channel by means of acoustic telemetry monitoring. Thirty percent of the fish tagged were not detected after the first 6 d following release and were assumed to have died or to have immediately emigrated away from platforms. Degrees of site fidelity varied widely among individuals, among species, and between platforms. Of the most abundant species tagged (cabezon Scorpaenichthys marmoratus, vermilion rockfish Sebastes miniatus, widow rockfish Sebastes entomelas, copper rockfish Sebastes caurinus, and greenspotted rockfish Sebastes chlorostictus), widow rockfish showed a high probability of being detected at platforms over a 2-year period. Vermilion rockfish emigrated away from the shallower Platform Gilda (64 m) faster than vermilion rockfish tagged at the deeper Platform Grace (93 m). Ten tagged individuals (eight vermilion rockfish, one copper rockfish, and one lingcod Ophiodon elongatus) moved between platforms (range = 5–15 km) and/or natural habitat, although a majority moved from a shallower platform to a deeper one. These movements further support evidence that (1) many reef-associated rockfishes make ontogenetic shifts to deeper water and (2) shallower platforms export fishes faster than deeper platforms. There was no indication of seasonal emigration, but there was evidence for seasonal differences in activity for vermilion rockfish, widow rockfish, and greenspotted rockfish. Observed movements of fishes between platforms and natural reef habitat indicate that they can navigate between these habitats and that platform habitat, despite having higher densities of conspecifics, may be of higher quality to some individuals than natural reefs.
The BASC system provides tools for the integrated mining and browsing of genetic, genomic and phenotypic data. This public resource hosts information on Brassica species supporting the Multinational ...Brassica Genome Sequencing Project, and is based upon five distinct modules, ESTDB, Microarray, MarkerQTL, CMap and EnsEMBL. ESTDB hosts expressed gene sequences and related annotation derived from comparison with GenBank, UniRef and the genome sequence of Arabidopsis. The Microarray module hosts gene expression information related to genes annotated within ESTDB. MarkerQTL is the most complex module and integrates information on genetic markers, maps, individuals, genotypes and traits. Two further modules include an Arabidopsis EnsEMBL genome viewer and the CMap comparative genetic map viewer for the visualization and integration of genetic and genomic data. The database is accessible at http://bioinformatics.pbcbasc.latrobe.edu.au.
In this paper, we study the distributed computational capabilities of device-to-device (D2D) networks. A key characteristic of D2D networks is that their topologies are reconfigurable to cope with ...network demands. For distributed computing, resource management is challenging due to limited network and communication resources, leading to inter-channel interference. To overcome this, recent research has addressed the problems of wireless scheduling, subchannel allocation, power allocation, and multiple-input multiple-output (MIMO) signal design, but has not considered them jointly. In this paper, unlike previous mobile edge computing (MEC) approaches, we propose a joint optimization of wireless MIMO signal design and network resource allocation to maximize energy efficiency. Given that the resulting problem is a non-convex mixed integer program (MIP) which is prohibitive to solve at scale, we decompose its solution into two parts: (i) a resource allocation subproblem, which optimizes the link selection and subchannel allocations, and (ii) MIMO signal design subproblem, which optimizes the transmit beamformer, transmit power, and receive combiner. Simulation results using wireless edge topologies show that our method yields substantial improvements in energy efficiency compared with cases of no offloading and partially optimized methods and that the efficiency scales well with the size of the network.
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