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20
Southampton, UK Reviewed by:
, 2012
"... doi: 10.3389/fmicb.2012.00142 Mining genomes of marine cyanobacteria for elements of zinc homeostasis ..."
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doi: 10.3389/fmicb.2012.00142 Mining genomes of marine cyanobacteria for elements of zinc homeostasis
Genome analysis Advance Access publication July 15, 2011
"... PGAT: a multistrain analysis resource for microbial genomes ..."
1389-2029/12 $58.00+.00 ©2012 Bentham Science Publishers Measures of Compositional Strand Bias Related to Replication Machinery and its Applications
"... Abstract: The compositional asymmetry of complementary bases in nucleotide sequences implies the existence of a mutational or selectional bias in the two strands of the DNA duplex, which is commonly shaped by strand-specific mechanisms in transcription or replication. Such strand bias in genomes, fr ..."
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Abstract: The compositional asymmetry of complementary bases in nucleotide sequences implies the existence of a mutational or selectional bias in the two strands of the DNA duplex, which is commonly shaped by strand-specific mechanisms in transcription or replication. Such strand bias in genomes, frequently visualized by GC skew graphs, is used for the computational prediction of transcription start sites and replication origins, as well as for comparative evolutionary genomics studies. The use of measures of compositional strand bias in order to quantify the degree of strand asymmetry is crucial, as it is the basis for determining the applicability of compositional analysis and comparing the strength of the mutational bias in different biological machineries in various species. Here, we review the measures of strand bias that have been proposed to date, including the GC skew, the B1 index, the predictability score of linear discriminant analysis for gene orientation, the signal-to-noise ratio of the oligonucleotide bias, and the GC skew index. These measures have been predominantly designed for and applied to the analysis of replication-related mutational processes in prokaryotes, but we also give research examples in eukaryotes.
Separating Drivers from Passengers in Whole Genome Analysis: Identification of Combinatorial Effects of Genes by Mining Knowledge Sources
"... Abstract—This study aimed to develop a new informatics platform for the discovery, recovery and multi-level analysis of the effects of individual genes and multiple gene combinations on pathophenotypes of bacteria. Natural language processing algorithms were employed to extract gene-disease associat ..."
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Abstract—This study aimed to develop a new informatics platform for the discovery, recovery and multi-level analysis of the effects of individual genes and multiple gene combinations on pathophenotypes of bacteria. Natural language processing algorithms were employed to extract gene-disease associations from PubMed literature and annotated genomes of bacteria with epidemic potential. From these associations gene virulence profiles were generated enabling the comparison of gene signatures within and across genomes. It allowed the identification of virulence genes and construction of their association networks as well as the detection of knowledge gaps. This proof-of-concept study confirmed the feasibility of our original approach for integrating bacterial genome level knowledge with published observations from clinical settings.
ARTICLE pubs.acs.org/est Fecal Contamination of Shallow Tubewells in Bangladesh Inversely Related to Arsenic
, 2011
"... bS Supporting Information ABSTRACT: The health risks of As exposure due to the installation of millions of shallow tubewells in the Bengal Basin are known, but fecal contamination of shallow aquifers has not systematically been examined. This could be a source of concern in densely populated areas w ..."
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bS Supporting Information ABSTRACT: The health risks of As exposure due to the installation of millions of shallow tubewells in the Bengal Basin are known, but fecal contamination of shallow aquifers has not systematically been examined. This could be a source of concern in densely populated areas with poor sanitation because the hydraulic travel time from surface water bodies to shallow wells that are low in As was previously shown to be considerably shorter than for shallow wells that are high in As. In this study, 125 tubewells 6-36m deep were sampled in duplicate for 18 months to quantify the presence of the fecal indicator Escherichia coli. On any given month, E. coli was detected at levels exceeding 1 most probable number per 100 mL in 19-64 % of all shallow tubewells, with a higher proportion
2011 DoD High Performance Computing Modernization Program Users Group Conference A Web-based High-Throughput Tool for Next-Generation Sequence Annotation
"... The availability of a large number of genome sequences, resulting from inexpensive, high-throughput next-generation sequencing platforms, has created the need for an integrated, fully-automated, rapid, and high-throughput annotation capability that is also easy-to-use. Here, we present a web-based s ..."
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The availability of a large number of genome sequences, resulting from inexpensive, high-throughput next-generation sequencing platforms, has created the need for an integrated, fully-automated, rapid, and high-throughput annotation capability that is also easy-to-use. Here, we present a web-based software application, Annotation of Genome Sequences (AGeS), which incorporates publicly-available and in-house-developed bioinformatics tools and databases, many of which are parallelized for high-throughput performance. The current version of AGeS provides annotations for bacterial genome sequences, and serves as a readily-accessible resource to Department of Defense (DoD) scientists for storing, annotating, and visualizing genomes of newly-sequenced pathogens of interest. The AGeS system is composed of two major components. The first component is a web-based application that provides a graphical user interface for managing users ’ input genomes, submitting annotation jobs, and visualizing results. Sequence contigs are uploaded as a multi-FASTA input file and submitted for annotation, and the resulting annotations are visualized through GBrowse. The input genome sequences and the annotation results are stored in a secure, customized database. The second component is a high-throughput annotation pipeline for finding the genomic regions that code for proteins, RNAs, and other genomic elements through a Do-It-Yourself Annotation framework. The pipeline also functionally annotates the protein-coding regions using an in-house-developed high-throughput pipeline, the Pipeline for Protein Annotation. The
REVIEW
, 2012
"... Chemoenzymatic synthesis of glycosaminoglycans: Re-creating, re-modeling and re-designing nature’s longest or most complex carbohydrate chains ..."
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Chemoenzymatic synthesis of glycosaminoglycans: Re-creating, re-modeling and re-designing nature’s longest or most complex carbohydrate chains
Original article The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes
"... The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze ..."
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The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. Oomycete and fungal genomes are obtained directly from GenBank, whereas bacterial genome sequences are downloaded from the A Systematic Annotation Package (ASAP) database that provides curation of genomes using comparative approaches. Curated lists of bacterial genes relevant to pathogenicity and avirulence are also provided. The Plant Pathogen Transcript Assemblies Database provides annotated assemblies of the transcribed regions of 82 eukaryotic genomes from publicly available single pass Expressed Sequence Tags. Data-mining tools are provided along with tools to create candidate diagnostic markers, an emerging use for genomic sequence data in plant pathology. The Plant Pathogen Ribosomal DNA (rDNA) database is a resource for pathogens that lack genome or transcriptome data sets and contains 131 755 rDNA sequences from GenBank for 17 613 species identified as plant pathogens and related
