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At least 271 records · Page 15Linked to original sources
PubMed2003

An interactive tool for extracting exons and SNP from genomic sequence: isolation of HCN1 and HCN3 ion channel genes.

Genome Analyzer (GenoA) with a relational database back-end, was developed to extract information from mammalian genomic sequences. This data mining and visualization tool-set enables laboratory bench scientists to identify and assemble virtual cDNA from genomic exon sequences, and provides a starting point to identify potential alternative splice variants and polymorphisms in silico. The study described in this paper demonstrates the use of GenoA to study human brain hyperpolarization-activated cation channel genes HCN1 and HCN3.

Amino Acid Sequence↗
PubMed2001

Genomic and spectral analyses of long to middle wavelength-sensitive visual pigments of common marmoset (Callithrix jacchus).

The genetic basis of red-green color vision of common marmoset (Callithrix jacchus) is not fully understood. Here, we have cloned and characterized the three alleles at a locus that encode the long to middle wavelength-sensitive (LWS/MWS) visual pigments of this species. Using in situ hybridization, we localized this locus to the telomeric region of the long arm of X chromosome. The three visual pigments achieve the wavelengths of maximal absorption at 561, 553, and 539 nm and fully explain the red-green color vision of the common marmoset. The 'tri-allelic single-locus X-chromosome' model operates under the unique phenomenon, known as blood chimerism.

Animals↗
PubMed2003

An improved probability mapping approach to assess genome mosaicism.

BACKGROUND: Maximum likelihood and posterior probability mapping are useful visualization techniques that are used to ascertain the mosaic nature of prokaryotic genomes. However, posterior probabilities, especially when calculated for four-taxon cases, tend to overestimate the support for tree topologies. Furthermore, because of poor taxon sampling four-taxon analyses suffer from sensitivity to the long branch attraction artifact. Here we extend the probability mapping approach by improving taxon sampling of the analyzed datasets, and by using bootstrap support values, a more conservative tool to assess reliability. RESULTS: Quartets of orthologous proteins were complemented with homologs from selected reference genomes. The mapping of bootstrap support values from these extended datasets gives results similar to the original maximum likelihood and posterior probability mapping. The more conservative nature of the plotted support values allows to focus further analyses on those protein families that strongly disagree with the majority or plurality of genes present in the analyzed genomes. CONCLUSION: Posterior probability is a non-conservative measure for support, and posterior probability mapping only provides a quick estimation of phylogenetic information content of four genomes. This approach can be utilized as a pre-screen to select genes that might have been horizontally transferred. Better taxon sampling combined with subtree analyses prevents the inconsistencies associated with four-taxon analyses, but retains the power of visual representation. Nevertheless, a case-by-case inspection of individual multi-taxon phylogenies remains necessary to differentiate unrecognized paralogy and shared phylogenetic reconstruction artifacts from horizontal gene transfer events.

Bacterial Proteins↗
PubMed2003

Amplification and overexpression of the L-MYC proto-oncogene in ovarian carcinomas.

Gene amplification is an important mechanism of oncogene activation in various human cancers, including ovarian carcinomas (OvCas). We used restriction landmark genomic scanning (RLGS) to detect amplified DNA fragments in the genomes of 47 primary OvCas. Visual analysis of the RLGS gel images revealed several OvCa samples with spots of greater intensity than corresponding spots from normal tissues, indicating possible DNA amplification in specific tumors. Two primary tumors (E1 and S12) shared four high-intensity spots. A recently developed informatics tool termed Virtual Genome Scans was used to compare the RLGS patterns in these tumors with patterns predicted from the human genome sequence. Virtual Genome Scans determined that three of the four fragments localized to chromosome 1p34-35, a region containing the proto-oncogene L-MYC. Sixty-eight primary OvCas, including 40 analyzed by RLGS, were screened by quantitative polymerase chain reaction (PCR) for possible amplification of L-MYC. Ten tumors with increased L-MYC copy number were identified, including tumor E1, which showed an approximately 24-fold increase in copy number compared to normal DNA. Southern analysis of several tumors confirmed the quantitative PCR results. Using sequence tagged site (STS) markers flanking L-MYC, increased DNA copy number in tumor E1 was found to span the region flanking L-MYC between D1S432 and D1S463 ( approximately 3.1 Mb). Other tumors showed amplification only at the L-MYC locus. Using oligonucleotide microarrays, L-MYC was found to be more frequently overexpressed in OvCas than either c-MYC or N-MYC relative to ovarian surface epithelium. Quantitative reverse transcriptase-PCR analysis confirmed elevated L-MYC expression in a substantial fraction of OvCas, including nine of nine tumors with increased L-MYC copy number. The data implicate L-MYC gene amplification and/or overexpression in human OvCa pathogenesis.

Base Sequence↗
PubMed2006

Genome-wide DNA polymorphism analyses using VariScan.

BACKGROUND: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. RESULTS: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers. CONCLUSION: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

Algorithms↗
PubMed2000

Visualization of repair of double-strand breaks in the bacteriophage T7 genome without normal DNA replication.

An in vitro system based on extracts of Escherichia coli infected with bacteriophage T7 is able to repair double-strand breaks in a T7 genome with efficiencies of 20% or more. To achieve this high repair efficiency it is necessary that the reaction mixtures contain molecules of donor DNA that bracket the double-strand break. Gaps as long as 1,600 nucleotides are repaired almost as efficiently as simple double-strand breaks. DNA synthesis was measured while repair was taking place. It was found that the amount of DNA synthesis associated with repair of a double-strand break was below the level of detection possible with this system. Furthermore, repair efficiencies were the same with or without normal levels of T7 DNA polymerase. However, the repair required the 5'-->3' exonuclease encoded by T7 gene 6. The high efficiency of DNA repair allowed visualization of the repaired product after in vitro repair, thereby assuring that the repair took place in vitro rather than during an in vivo growth step after packaging.

Bacteriophage T7↗
PubMed1997

EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism.

The Encyclopedia of Genes and Metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of Escherichia coli. It describes 2970 genes of E.coli, 547 enzymes encoded by these genes, 702 metabolic reactions that occur in E.coli and the organization of these reactions into 107 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc spans the space from sequence to function to allow scientists to investigate an unusually broad range of questions. EcoCyc can be thought of as both an electronic review article because of its copious references to the primary literature, and as an in silicio model of E.coli metabolism that can be probed and analyzed through computational means.

Amino Acid Sequence↗
PubMed1998

EcoCyc: Encyclopedia of Escherichia coli genes and metabolism.

The encyclopedia of Escherichia coli genes and metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of E.coli. The database describes 3030 genes of E.coli , 695 enzymes encoded by a subset of these genes, 595 metabolic reactions that occur in E.coli, and the organization of these reactions into 123 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc can be thought of as an electronic review article because of its copious references to the primary literature, and as a (qualitative) computational model of E.coli metabolism. EcoCyc is available at URL http://ecocyc.PangeaSystems.com/ecocyc/

Computer Graphics↗
PubMed2006

Browsing repeats in genomes: Pygram and an application to non-coding region analysis.

BACKGROUND: A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires specialized methods, including visualization techniques, to achieve optimum exploratory power. RESULTS: This article presents Pygram, a new visualization application for investigating the organization of repeated sequences in complete genome sequences. The application projects data from a repeat index file on the analysed sequences, and by combining this principle with a query system, is capable of locating repeated sequences with specific properties. In short, Pygram provides an efficient, graphical browser for studying repeats. Implementation of the complete configuration is illustrated in an analysis of CRISPR structures in Archaea genomes and the detection of horizontal transfer between Archaea and Viruses. CONCLUSION: By proposing a new visualization environment to analyse repeated sequences, this application aims to increase the efficiency of laboratories involved in investigating repeat organization in single genomes or across several genomes.

Codon↗
PubMed1999

Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.

The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactions into 129 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc has many references to the primary literature, and is a (qualitative) computational model of E. coli metabolism. EcoCyc is available at URL http://ecocyc. PangeaSystems.com/ecocyc/

Classification↗
PubMed2025

APAV: An advanced pangenome analysis and visualization toolkit.

Traditional pangenome analysis focuses on gene presence/absence variations (gene PAVs). However, the current methods for gene PAV analysis are insensitive to detect small but valuable mutations within gene regions, and they overlook variations in intergenic regions. Additionally, the visual inspection of PAVs is an important but time-consuming step for pangenome analysis and result interpretation. To address these issues, we present APAV, an advanced toolkit designed for comprehensive PAV analysis and visualization. It integrates gene element-level PAV analysis and provides PAV analysis for arbitrary given regions in a genome. The resulted PAV profile can be visualized and investigated interactively with reports in HTML format, enabling researchers to conveniently verify sequencing read depth, target region coverage, and intervals of absence for each PAV. Furthermore, APAV offers various subsequent analysis and visualization functions based on the PAV profile table, including basic statistics, sample clustering, genome size estimation, and phenotype association analysis. We demonstrated the capability of APAV with pangenome analysis of tumor genomes and rice genomes. Performing PAV analysis at the element level not only provides more accurate information about the variations but also uncovers a larger number of variations for the phenotype-genotype association studies. In the rice genome analysis, we identified over twenty thousand distributed genes and more than fifty thousand distributed genetic elements. In the tumor genome analysis, element-level analysis revealed approximately three times as many phenotype-related genes as gene-level analysis. This indicates that altering the PAV unit from genes to smaller segments or elements can lead to more biological insights.

Software↗
PubMed2005

Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops.

BACKGROUND: Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. RESULTS: Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. CONCLUSION: The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.

Agrobacterium tumefaciens↗
PubMed2003

The PEDANT genome database.

The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based user interface. One hundred and seventy seven completely sequenced and unfinished genomes have been processed so far, including large eukaryotic genomes (mouse, human) published recently. In this contribution, we describe the current status of the PEDANT database and novel analytical features added to the PEDANT server in 2002. Those include: (i) integration with the BioRS data retrieval system which allows fast text queries, (ii) pre-computed sequence clusters in each complete genome, (iii) a comprehensive set of tools for genome comparison, including genome comparison tables and protein function prediction based on genomic context, and (iv) computation and visualization of protein-protein interaction (PPI) networks based on experimental data. The availability of functional and structural predictions for 650 000 genomic proteins in well organized form makes PEDANT a useful resource for both functional and structural genomics.

Animals↗
PubMed2004

Representing GC variation along eukaryotic chromosomes.

Genome sequencing now permits direct visual representation, at any scale, of GC heterogeneity along the chromosomes of several higher eukaryotes. Plots can be easily obtained from the chromosomal sequences, yet sequence releases of mammalian or plant chromosomes still tend to use small scales or window sizes that obscure important large-scale compositional features. To faithfully reveal, at one glance, the compositional variation at a given scale, we have devised a simple scheme that combines line plots with color-coded shading of the regions underneath the plots. The scheme can be applied to different eukaryotic genomes to facilitate their comparison, as illustrated here for a sample of chromosomes chosen from seven selected species. As a complement to a previously published compact view of isochores in the human genome sequence, we include here an analogous map for the recently sequenced mouse genome, and discuss the contribution of repetitive DNA to the GC variation along the plots. Supplementary information, including a database of color-coded GC profiles for all recently sequenced eukaryotes and the program draw_chromosomes_gc.pl used to obtain them, are available at.

Animals↗
PubMed1990

Patterns of expression of position-dependent integrated transgenes in mouse embryo.

The abilities to introduce foreign DNA into the genome of mice and to visualize gene expression at the single-cell level underlie a method for defining individual elements of a genetic program. We describe the use of an Escherichia coli lacZ reporter gene fused to the promoter of the gene for hypoxanthine phosphoribosyl transferase that is expressed in all tissues. Most transgenic mice (six of seven) obtained with this construct express the lacZ gene from the hypoxanthine phosphoribosyltransferase promoter. Unexpectedly, however, the expression is temporally and spatially regulated. Each transgenic line is characterized by a specific, highly reproducible pattern of lacZ expression. These results show that, for expression, the integrated construct must be complemented by elements of the genome. These elements exert dominant developmental control on the hypoxanthine phosphoribosyltransferase promoter. The expression patterns in some transgenic mice conform to a typological marker and in others to a subtle combination of typology and topography. These observations define discrete heterogeneities of cell types and of certain structures, particularly in the nervous system and in the mesoderm. This system opens opportunities for developmental studies by providing cellular, molecular, and genetic markers of cell types, cell states, and cells from developmental compartments. Finally this method illustrates that genes transduced or transposed to a different position in the genome acquire different spatiotemporal specificities, a result that has implications for evolution.

Animals↗
PubMed2027

Systematic Analysis of Tumor Microenvironment Using IOBR.

The Immuno-Oncology Biological Research (IOBR) package is an R-based analysis tool for exploring the tumor microenvironment (TME) and its influence on anti-tumor immunity. Built for high-throughput data-spanning both transcriptomic and genomic profiles-IOBR integrates six analytical modules, including transcriptomic data preprocessing, TME profiling, TME pattern identification, ligand-receptor interaction analysis, genome-TME interaction assessment, and visualization. In this chapter, we walk through a multi-omics workflow using example datasets, illustrating data preparation, distribution analyses, result interpretation, and graphical output. IOBR is open source and is available at https://github.com/IOBR/IOBR and a detailed GitBook ( https://iobr.github.io/book/ ) offers a complete manual and analysis guide for each function.

Tumor Microenvironment↗
PubMed1996

Site-specific induction and repair of benzo[a]pyrene diol epoxide DNA damage in human H-ras protooncogene as revealed by restriction cleavage inhibition.

Most genotoxic DNA base modifications localized at key genomic sequences constitute the molecular alterations crucial or mutagenesis and tumorigenesis. We have utilized lesion-rendered inhibition of restriction endonuclease cleavage for the analysis of site-specific DNA damage induced by (+/-)-7,8-dihydroxy-anti-9, 10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (benzo[a]pyrene diol epoxide, anti-BPDE) in human genes. The H-ras protooncogene and insulin gene sequences were used as targets for modification in vitro and in vivo. Selective induction of individual facultative bands, resulting from covalent modification of the cognate recognition sites, was observed in modified plasmid DNA for a number of restriction nucleases. The ras gene-specific damage, at the PstI, BstYI, NotI and BstEII recognition sites, was visualized and quantitated in human genomic DNA adducted by anti-BPDE. Repair of lesions at hexanucleotide sequences and/or regions surrounding the restriction site, was assessed as a gradual disappearance of facultative bands in DNA from repair-proficient human fibroblasts exposed to the carcinogen in confluent culture. Efficiency of the PstI site-specific repair was compared at low and high levels of initial damage. Higher genotoxic dose caused a decrease in the extent of adduct removal from the bulk DNA, while the specific site of the ras gene was still subject to fast repair. No measurable PstI site-specific repair was detected in the insulin gene. These results show the region-selective induction of bulky anti-BPDE DNA damage in non-related genomic targets and suggest that repair of these lesions in human cells proceeds with the efficiency tightly controlled at different levels of initial genotoxic load.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1999

bioWidgets: data interaction components for genomics.

MOTIVATION: The presentation of genomics data in a perspicuous visual format is critical for its rapid interpretation and validation. Relatively few public database developers have the resources to implement sophisticated front-end user interfaces themselves. Accordingly, these developers would benefit from a reusable toolkit of user interface and data visualization components. RESULTS: We have designed the bioWidget toolkit as a set of JavaBean components. It includes a wide array of user interface components and defines an architecture for assembling applications. The toolkit is founded on established software engineering design patterns and principles, including componentry, Model-View-Controller, factored models and schema neutrality. As a proof of concept, we have used the bioWidget toolkit to create three extendible applications: AnnotView, BlastView and AlignView.

Amino Acid Sequence↗