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Results for “genome visualization”

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PubMed2004

Adplot: detection and visualization of repetitive patterns in complete genomes.

MOTIVATION: Repetitive DNA sequences are abundant in genomes and efficient mining of significant repeats is important as the first step of repetitive sequence research. Although many computational tools for the purpose, either automatic or visualization ones, have been developed, detection and analysis of approximate repeats are still non-trivial task. RESULTS: Auto Dot PLOT (Adplot), a dotplot-like repetitive pattern visualization program with a window filtering based on iid Bernoulli trials, is developed and applied to yeast chromosomes and human T cell receptor locus sequence. Typical examples found in yeast chromosomes 1 and 10 and a tandem repeat of periods longer than 10,000 bp in human T cell receptor locus are presented. A complex structure composed of both direct and palindromic repeats found in yeast chromosome 10 is also visualized as specific dot pattern. Computational time measured by a Pentium 3 PC for each yeast auto chromosome with a standard parameter setting is linearly scaled and below 10 s per one chromosome, indicating efficiency of the program. From the examples, it is shown that Adplot can visualize approximate local repeat structures and give us a diagnosis power for inferring a duplicational history of repeats. AVAILABILITY: Adplot can be obtained by an e-mail request.

Algorithms↗
PubMed2003

DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization.

The DiagHunter and GenoPix2D applications work together to enable genomic comparisons and exploration at both genome-wide and single-gene scales. DiagHunter identifies homologous regions (synteny blocks) within or between genomes. DiagHunter works efficiently with diverse, large datasets to predict extended and interrupted synteny blocks and to generate graphical and text output quickly. GenoPix2D allows interactive display of synteny blocks and other genomic features, as well as querying by annotation and by sequence similarity.

Algorithms↗
PubMed2004

Java-based application framework for visualization of gene regulatory region annotations.

MOTIVATION: The genome sequences of several organisms are either complete, or being sequenced. Each genome needs to be integrated with various types of annotations, e.g. locations of genes, promoters and other functional elements such as transcriptional regulatory elements. A robust application framework will be useful for developing web-based applications to visualize various genome annotations. RESULTS: We developed genome data visualization toolkit (GDVTK) as an application framework that consists of a set of data structures and core classes, using Java technology. GDVTK is a sound framework for developing web-based applications to present the gene regulatory region annotations in visual form. The current version of GDVTK consists of eight packages and 38 Java classes that are portable, reusable and extensible for plugging in new data sources and models. We implemented GDVTK for visualization of promoter annotations in Mammalian Promoter Database (MPromDb), a web-based gene-regulatory information server. AVAILABILITY: GDVTK is available under GNU general public license. Source code and software documentation can be found at the URL http://bioinformatics.med.ohio-state.edu/GDVTK.

Computer Graphics↗
PubMed2000

Computation and visualization of degenerate repeats in complete genomes.

The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter family of programs described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance, interactive visualization, and simple interfacing to other analysis programs.

Algorithms↗
PubMed2026

Clinical Variant Interpretation with the Integrative Genomics Viewer (IGV) for Molecular Pathologists.

The integrative genomics viewer (IGV) is a pivotal tool in clinical genomics, enabling the visualization and interpretation of complex sequencing data. Bringing clinical knowledge to bear with visual evaluation of sequencing results is the primary means by which molecular pathologists and other professionals assess and finalize cases. A variety of software tools can assist, but their relationship to the underlying data must be understood and applied systematically. This study includes essential background on next-generation sequencing (NGS) data file types (e.g., FASTQ, BAM, VCF) with a discussion of their format and purpose. We then describe features of IGV that derive nuances from these files. We utilize a series of curated practical cases based on clinical vignettes through which the reader will interact with clinical NGS sequencing data using the IGV software to review various types of clinically relevant variants relative to the human reference genome. These clinical vignettes have been curated to describe examples of some of the complexities of interpretation of genomic data, and how utilizing IGV as part of a routine workflow can provide additional interpretive information for variants beyond routine bioinformatic software algorithm variant calls. The visual inspection of genomic variants utilizing the tools within IGV can unmask subtle contextual cues (i.e., variant allele frequency, strand bias, tissue-specific context) that can influence the interpretation of genomic variants. Although this study focuses on using IGV for the detection and interpretation of somatic variants, the provided applications can be extrapolated for use in the germline setting, including analysis of complex variants and detection of mosaicism.

Humans↗
PubMed1999

Trypanosoma brucei: improved detection of nuclear transcripts reveals a genomic position effect on nuclearly accumulating NEO RNAs visualized in stably transformed cells.

Köhler, S. 1999. Trypanosoma brucei: Improved detection of nuclear transcripts reveals a genomic position effect on nuclearly accumulating NEO RNAs visualized in stably transformed cells. Experimental Parasitology 92, 249-262. An improved fluorescent in situ hybridization method was used to visualize accumulations of nuclear RNA in procyclic Trypanosoma brucei that were stably transformed with a bacterial gene encoding neomycin phosphotransferase (NEO). In both wild-type trypanosomes and NEO transformants, nuclear accumulations of endogenous RRNAs were restricted to a ring-shaped subcompartment (nucleolus) of the nucleus. A nucleolar localization was also illuminated for NEO RNAs of trypanosomal transformants mediating their NEO transcription from the endogenous RRNA gene cluster of the T. brucei genome. In contrast, stably transformed trypanosomes generating their NEO transcripts from protein-coding areas of the T. brucei genome displayed a single dot-like accumulation of NEO transcripts, which was located in close proximity to the trypanosomal nucleolus. This pattern was observed in transformants employing either the promoter region of a protein-coding PARP transcription unit or the trypanosomal RRNA promoter for NEO transcription. Apparently, the exact location of nuclearly accumulating NEO transcripts varied among different trypanosomal transformants and relied explicitly on the genomic position of the NEO gene. These results imply that T. brucei possesses distinctive pathways for its nuclear RNA metabolism, which is consistent with a spatio-functional organization of the parasite's nucleus.

Animals↗
PubMed1988

A novel beta-thalassemia frameshift mutation (codon 14/15), detectable by direct visualization of abnormal restriction fragment in amplified genomic DNA.

A new frameshift mutation due to an insertion of G between codon 14/15 of the beta-globin gene was found in two unrelated Chinese patients with Cooley's anemia. The first patient (W.S.) was homozygous for haplotype 5 (Chinese) and carried a codon 41/42 (four base pair deletion) mutant, while the second patient (C.K.) was homozygous for haplotype 2 (Chinese), and also had a codon 17 (A----T) nonsense mutation. Molecular cloning and M13 sequencing of the beta gene in patient W.S. revealed that the new mutant was found in a beta-globin gene framework type 3 (Asian). Direct sequencing was performed on polymerase chain reaction-amplified genomic DNA from patient C.K. With the new mutation, an additional BstNI or EcoRII recognition site is generated and the abnormal restriction fragment (134 basepair) can be directly visualized on polyacrylamide gel electrophoresis of the amplified genomic DNA.

Base Sequence↗
PubMed1994

Future of germ cell cytogenetics.

The celebration of the 25th Anniversary of the Environmental Mutagen Society provides an excellent opportunity to assess the status of research in a broad range of areas, with an emphasis on the directions in which they are going. This chapter concentrates on the analysis of chromosomal alterations in mammalian germ cells. The future developments in germ cell cytogenetics research will build heavily upon techniques developed over the past 25 years. With these it is possible to assess numerical and structural alterations in the male in differentiating spermatogonia, spermatocytes, and post-meiotic cells (at the first cleavage division) and for the female in oocytes and the zygote. The most predictable advances will be in the identification of specific alterations through FISH of interphase spermatozoa in humans and further improvements with the human sperm/hamster egg in vitro fertilization technique. Of particular importance is the fact that this will allow for the study of effects in human germ cells. From a more speculative viewpoint it might be possible to assess the role of particular genomic organization on genetic outcomes by direct observation; these might include genomic imprinting and the visual separation of male and female genomes. The overall aim of germ cell cytogenetic studies will remain as improving our ability to identify and estimate the true genetic risk in humans.

Animals↗
PubMed2002

Visualizing metabolic activity on a genome-wide scale.

MOTIVATION: To enhance the exploration of gene expression data in a metabolic context, one requires an application that allows the integration of this data and which represents this data in a (genome-wide) metabolic map. The layout of this metabolic map must be highly flexible to enable discoveries of biological phenomena. Moreover, it must allow the simultaneous representation of additional information about genes and enzymes. Since the layout and properties of existing maps did not fulfill our requirements, we developed a new way of representing gene expression data in metabolic charts. RESULTS: ViMAc generates user-specified (genome-wide) metabolic maps to explore gene expression data. To enhance the interpretation of these maps information such as sub-cellular localization is included. ViMAc can be used to analyse human or yeast expression data obtained with DNA microarrays or SAGE. We introduce our metabolic map method and demonstrate how it can be applied to explore DNA microarray data for yeast. AVAILABILITY: ViMAc is freely available for academic institutions on request from the authors.

Computational Biology↗
PubMed2003

Comparing bacterial genomes through conservation profiles.

We constructed two-dimensional representations of profiles of gene conservation across different genomes using the genome of Escherichia coli as a model. These profiles permit both the visualization at the genome level of different traits in the organism studied and, at the same time, reveal features related to the genomes analyzed (such as defective genomes or genomes that lack a particular system). Conserved genes are not uniformly distributed along the E. coli genome but tend to cluster together. The study of gene distribution patterns across genomes is important for the understanding of how sets of genes seem to be dependent on each other, probably having some functional link. This provides additional evidence that can be used for the elucidation of the function of unannotated genes. Clustering these patterns produces families of genes which can be arranged in a hierarchy of closeness. In this way, functions can be defined at different levels of generality depending on the level of the hierarchy that is studied. The combined study of conservation and phenotypic traits opens up the possibility of defining phenotype/genotype associations, and ultimately inferring the gene or genes responsible for a particular trait.

Chromosome Mapping↗
PubMed2004

VISTA: computational tools for comparative genomics.

Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/vista/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, to submit their own sequences of interest to several VISTA servers for various types of comparative analysis and to obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein.

Binding Sites↗
PubMed2002

Analysis of common k-mers for whole genome sequences using SSB-tree.

As sequenced genomes become larger and sequencing process becomes faster, there is a need to develop a tool to analyze sequences in the whole genomic scale. However, on-memory algorithms such as suffix tree and suffix array are not applicable to the analysis of whole genome sequence set, since the size of individual whole genome ranges from several million base pairs to hundreds billion base pairs. In order to effectively manipulate the huge sequence data, it is necessary to use the indexed data structure for external memory. In this paper, we introduce a workbench called SequeX for the analysis and visualization of whole genome sequences using SSB-tree (Static SB-tree). It consists of two parts: the analysis query subsystem and the visualization subsystem. The query subsystem supports various transactions such as pattern matching, k-occurrence, and k-mer analysis. The visualization subsystem helps biologists to easily understand whole genome structure and feature by sequence viewer, annotation viewer, CGR (Chaos Game Representation) viewer, and k-mer viewer. The system also supports a user-friendly programming interface based on Java script for batch processing and the extension for a specific purpose of a user. SequeX can be used to identify conserved genes or sequences by the analysis of the common k-mers and annotation. We analyze the common k-mer for 72 microbial genomes announced by Entrez, and find an interesting biological fact that the longest common k-mer for 72 sequences is 11-mer, and only 11 such sequences exist. Finally we note that many common k-mers occur in conserved region such as CDS, rRNA, and tRNA.

Archaea↗
PubMed2004

The visual language of synteny.

The study of polygenic disorders such as cardiovascular and metabolic diseases requires access to vast amounts of experimental and in silico data. Where animal models of disease are being used, visualization of syntenic genome regions is one of the most important tools supporting data analysis. We define what is required to visualize synteny in terms of the data being displayed, the screen layout, and user interaction. We then describe a prototype visualization tool, SyntenyVista, which provides integrated access to quantitative trait loci, microarray, and gene datasets. We believe that SyntenyVista is a significant step towards an improved representation of comparative genomics data.

Algorithms↗
PubMed2005

BacMap: an interactive picture atlas of annotated bacterial genomes.

BacMap is an interactive visual database containing fully labeled, zoomable and searchable chromosome maps from more than 170 bacterial (archaebacterial and eubacterial) species. It uses a recently developed visualization tool (CGView) to generate high-resolution circular genome maps from sequence feature information. Each map includes an interface that allows the image to be expanded and rotated. In the default view, identified genes are drawn to scale and colored according to coding directions. When a region of interest is expanded, gene labels are displayed. Each label is hyperlinked to a custom 'gene card' which provides several fields of information concerning the corresponding DNA and protein sequences. Each genome map is searchable via a local BLAST search and a gene name/synonym search. BacMap is freely available at http://wishart.biology.ualberta.ca/BacMap/.

Chromosome Mapping↗
PubMed2005

Karyotypic analysis of adult pluripotent stem cells.

Three categories of precursor cells have been identified in postnatal mammals: tissue-committed progenitor cells, germ layer lineage-committed stem cells and lineage-uncommitted pluripotent stem cells. Progenitor cells are the immediate precursors of differentiated tissues. Germ layer lineage stem cells can be induced to form multiple cell types belonging to their respective ectodermal, mesodermal, and endodermal embryological lineages. Pluripotent stem cells will form somatic cell types from all three primary germ layer lineages. Progenitor cells demonstrate a finite life span before replicative senescence and cell death occur. Both germ layer lineage stem cells and pluripotent stem cells are telomerase positive and display extensive capabilities for self-renewal. Stem cells which undergo such extensive replication have the potential for undergoing mutations that may subsequently alter cellular functions. Gross mutations in the genome may be visualized as chromosomal aneuploidy and/or chromosomes that appear aberrant. This study was designed to determine whether any gross genomic mutations occurred within the adult pluripotent stem cells. Karyotypic analysis was performed using pluripotent stem cells purified from adult male rats using established procedures. Giemsa Banding was used in conjunction with light microscopy to visualize metaphase chromosome spreads. To date over 800 metaphase spreads have been analyzed. We found that the metaphase spreads averaged 42 chromosomes and concluded that these pluripotent stem cells isolated from adult rats have a normal karyotype.

Animals↗
PubMed1995

Accessibility to tissue-specific genes from methylation profiles of mouse brain genomic DNA.

The DNA methylation status of a large number of genomic loci is visualized simultaneously and quantitatively as two-dimensional gel spots in the newly developed restriction landmark genomic scanning with a methylation-sensitive restriction enzyme (RLGS-M). Here, we demonstrate that RLGS-M using NorI as a methylation-sensitive enzyme could also scan gene loci of mammalian genomes, since almost all of the NotI loci corresponding to randomly chosen RLGS-M spots were located near or in transcriptional units (6 out of 7 NotI-linking clones) when mouse brain genomic DNA was used. This supports the previous prediction that most NotI sites are located in CpG islands (Lindsay and Bird, Nature 1987, 327, 336-338). Furthermore, beginning with RLGS-M spots we examined how to approach their corresponding RNA messages, whose expression may be associated with methylation. We compared RLGS-M patterns among various developmental stages of the mouse brain from embryonic day 9.5 to postnatal 8 weeks or among in vitro cell lines, and detected alterations of RLGS-M spots which were due to methylation of NotI sites. Two experiments using NotI-linking clones or polymerase chain reaction (PCR) were carried out to approach to their corresponding RNA messages. Consequently, we isolated two PCR-amplified clones (# 15 and # 91) which corresponded to methylatable loci and gave positive signals to mRNA from the adult brain. Furthermore, we identified two NotI-linking clones (C211 and C198) whose corresponding NotI loci localized near or at transcriptional units and were methylated in cell lines.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2002

Achieving congruency of phylogenetic trees generated by W-curves of genomic sequences.

Comparative genomic analysis at its most fundamental level involves alignment and analysis of linear strings of DNA. Many useful and powerful tools, such as BlastN and ClustalW are able to respectively, search for, and align similar strings of DNA from a variety of species. However, interesting genomic patterns cannot be immediately visualized within the information contact embedded in long genomic strings without extensive a priori knowledge. More problematic is the question of whether we will be able to crystallize long genomic sequences and analyze their true secondary and tertiary structures. It is, of course, these putative motifs that are binding to the three-dimensional structures of proteins and inducing replication and transcription events. The W-curve is a numerical mapping algorithm that allows one to geometrically visualize the information content of genomic motifs. Patterns of ALU, LINES, SINEs, and duplication sequences may be easily visualized with the W-curve. It is our hope that this pattern recognition algorithm will lead to visualization tools to track the evolutionary history of motif patterns. The combinatorics of DNA motif crossover-recombination events will be more easily followed as we continue to sequence more and more genomes. In our laboratory we are currently collaborating with mathematicians and computer scientists to develop and test tools, such as the W-curve, for analyzing patterns of long genomic sequences. In this paper, we examine the limitations of using the W-curve to infer the phylogenetic history of species.

Bacteria↗
PubMed2004

Information for the Coordinates of Exons (ICE): a human splice sites database.

We present a comprehensive database, Information for the Coordinates of Exons (ICE), of genomic splice sites (SSs) for 10,803 human genes. ICE contains 91,846 pairs of donor acceptor sites, supported by the alignment of "full-length" human mRNAs (including transcript variants) on human genomic sequences. ICE represents the largest collection of human SSs known to date and provides a significant resource to both molecular biologists and bioinformaticians alike. A user can visualize and extract genomic sequences around SSs of the donor acceptor pairs and can also visualize the primary structure of individual genes. We list in this article the 22 most frequently found canonical and noncanonical splice sites. The top four most represented donor acceptor pairs (GT-AG, GC-AG, AT-AC, and GT-GG) accounted for 99.16% of our data set. In addition, we calculated the SS matrix models for the three most common donor acceptor pairs. The database is focused on providing SSs and surrounding sequence information, associated SS and sequence characteristics, and relation to overall transcript structure. It allows targeted search and presents evidence for the gene structure.

Computational Biology↗