PGV - Prokaryotic Genome Viewer

Recent sequencing of genomes of several microorganisms provides an opportunity to have access to huge volumes of data stored in various databases. This has resulted in the development of various computational and visualization tools to aid in retrieval and analysis of data. Development of user friendly genome data mapping and visualization tools facilitates researchers to closely examine various features of genes and make inferences from the displayed data efficiently. PGV - Prokaryotic Genome Viewer is a Java based web application tool capable of generating high quality interactive circular chromosome maps. With simple mouse roll over tasks on the interested region on the displayed map, the user is provided with features such as feature labeling, multi-fold zooming, image rotation and hyperlinking to different information resources. The tool is capable of instantaneously generating maps using user-supplied sequence data.     

Circular genome visualization and exploration using CGView

SUMMARY: CGView (Circular Genome Viewer) is a Java application and library for generating high-quality, zoomable maps of circular genomes. It converts XML or tab-delimited input into a graphical map (PNG, JPG or Scalable Vector Graphics format), complete with sequence features, labels, legends and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any Web browser, allowing rapid genome browsing and facilitating data sharing. AVAILABILITY: CGView (the standalone application, library or applet), sample input, sample maps and documentation can be obtained from http://wishart.biology.ualberta.ca/cgview/ CONTACT: david.wishart@ualberta.ca.     

Plant genome resources at the national center for biotechnology information

The National Center for Biotechnology Information (NCBI) integrates data from more than 20 biological databases through a flexible search and retrieval system called Entrez. A core Entrez database, Entrez Nucleotide, includes GenBank and is tightly linked to the NCBI Taxonomy database, the Entrez Protein database, and the scientific literature in PubMed. A suite of more specialized databases for genomes, genes, gene families, gene expression, gene variation, and protein domains dovetails with the core databases to make Entrez a powerful system for genomic research. Linked to the full range of Entrez databases is the NCBI Map Viewer, which displays aligned genetic, physical, and sequence maps for eukaryotic genomes including those of many plants. A specialized plant query page allow maps from all plant genomes covered by the Map Viewer to be searched in tandem to produce a display of aligned maps from several species. PlantBLAST searches against the sequences shown in the Map Viewer allow BLAST alignments to be viewed within a genomic context. In addition, precomputed sequence similarities, such as those for proteins offered by BLAST Link, enable fluid navigation from unannotated to annotated sequences, quickening the pace of discovery. NCBI Web pages for plants, such as Plant Genome Central, complete the system by providing centralized access to NCBI's genomic resources as well as links to organism-specific Web pages beyond NCBI.     

The UCSC Genome Browser Database

The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.     

MuGeN: simultaneous exploration of multiple genomes and computer analysis results

MOTIVATION: The availability of increasing amounts of sequence data about completely sequenced genomes spurs the development of new methods in the fields of automated annotation, and of comparative genomics. Tools allowing the visualization of results produced by analysis methods, superimposed on possibly annotated sequence data, and enabling synchronized navigation in multiple genomes, provide new means for interactive genome exploration. This kind of visual inspection can be used as a basis to assess the quality of new analysis algorithms, or to discover genome portions to be subjected to in-depth studies. RESULTS: We propose a software package, MuGeN, built for navigating through multiple annotated genomes. It is capable of retrieving annotated sequences in several formats, stored in local files, or available in databases over the network. From these, it then generates an interactive display, or an image file, in most common formats suitable for printing, further editing or integrating in Web pages. Genome maps may be mixed with computer analysis results loaded from XML files, whose format is generic enough to be adapted to a majority of sequence oriented analysis methods. AVAILABILITY: MuGeN is available at http://www-mig.jouy.inra.fr/bdsi/MuGeN.     

AtDB, the Arabidopsis thaliana database, and graphical-web-display of progress by the Arabidopsis Genome Initiative.

AtDB, the Arabidopsis thaliana Database, has a primary role to provide public access to the collected genomic information for A. thaliana via the World Wide Web (URL: http://genome-www.stanford. edu/ ). AtDB presents interactive physical and genetics maps that are hyperlinked with detailed information about the clones and markers placed on these maps. A large literature collection on Arabidopsis , contact information on researchers worldwide, laboratory method manuals and other information useful to plant molecular biologists are also provided. This paper discusses the database-driven clickable displays that provide easy navigation within a variety of genomic maps, including those summarizing progress of the international Arabidopsis genomic sequencing effort, AGI (the Arabidopsis Genome Initiative). The interface uses client-side hyperlinked GIF-images that direct the user to detailed database-information. A new BLAST service is also described. This gives users access to the thousands of Arabidopsis BAC clone end-sequences and includes hyperlinked images summarizing the search results. The linking of genetic and physically mapped regions and their sequence into information for loci within that region is an ongoing goal for this project.     

Interactive microbial genome visualization with GView

SUMMARY: GView is a Java application for viewing and examining prokaryotic genomes in a circular or linear context. It accepts standard sequence file formats and an optional style specification file to generate customizable, publication quality genome maps in bitmap and scalable vector graphics formats. GView features an interactive pan-and-zoom interface, a command-line interface for incorporation in genome analysis pipelines, and a public Application Programming Interface for incorporation in other Java applications. AVAILABILITY: GView is a freely available application licensed under the GNU Public License. The application, source code, documentation, file specifications, tutorials and image galleries are available at http://gview.ca.     

iPath: interactive exploration of biochemical pathways and networks

iPath is an open-access online tool (http://pathways.embl.de) for visualizing and analyzing metabolic pathways. An interactive viewer provides straightforward navigation through various pathways and enables easy access to the underlying chemicals and enzymes. Customized pathway maps can be generated and annotated using various external data. For example, by merging human genome data with two important gut commensals, iPath can pinpoint the complementarity of the host-symbiont metabolic capacities.     

SGD: Saccharomyces Genome Database.

The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic sequence, its genes and their products, the phenotypes of its mutants, and the literature supporting these data. The amount of information and the number of features provided by SGD have increased greatly following the release of the S.cerevisiae genomic sequence, which is currently the only complete sequence of a eukaryotic genome. SGD aids researchers by providing not only basic information, but also tools such as sequence similarity searching that lead to detailed information about features of the genome and relationships between genes. SGD presents information using a variety of user-friendly, dynamically created graphical displays illustrating physical, genetic and sequence feature maps. SGD can be accessed via the World Wide Web at http://genome-www.stanford.edu/Saccharomyces/     

Advances in the human genome project – A review

While celebrating its fifth official birthday last year it seems that the Human Genome Project (HGP) has and will continue to yield important biochemical information to mankind. It is exhilarating to think about the transition from studying genome structure to understanding genome function. The collective actions of information dessimination, technology development for efficient and faster sequencing, high-volume sequencing and developing model organisms has led to its success sofar. Various genome-wide STS-based human maps were completed in 1995, including a genetic map, a YAC map, a RH map with, and an integrated YAC-RH genetic map. These maps provide comprehensive frameworks for positioning additional loci, with the current genetic and RH maps spanning essentially 100% of the human genome and the YAC maps covering 95%. Few genes, however, have yet been localized on these framework maps. To date the Human Genome Project has experienced gratifying success. The technology and data produced by the genome project will provide a strong stimulus to broad areas of biological research and biotechnology. However, enormous challenges remain.     

The institute for genomic research Osa1 rice genome annotation database

We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were identified using a series of computational methods developed for Arabidopsis (Arabidopsis thaliana) that were modified for use with the rice genome. In release 3 of our annotation, we identified 57,915 genes, of which 14,196 are related to transposable elements. Of these 43,719 non-transposable element-related genes, 18,545 (42.4%) were annotated with a putative function, 5,777 (13.2%) were annotated as encoding an expressed protein with no known function, and the remaining 19,397 (44.4%) were annotated as encoding a hypothetical protein. Multiple splice forms (5,873) were detected for 2,538 genes, resulting in a total of 61,250 gene models in the rice genome. We incorporated experimental evidence into 18,252 gene models to improve the quality of the structural annotation. A series of functional data types has been annotated for the rice genome that includes alignment with genetic markers, assignment of gene ontologies, identification of flanking sequence tags, alignment with homologs from related species, and syntenic mapping with other cereal species. All structural and functional annotation data are available through interactive search and display windows as well as through download of flat files. To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org.     

KAREBrowser: SNP database of Korea Association REsource Project

The International HapMap Project and the Human Genome Diversity Project (HGDP) provide plentiful resources on human genome information to the public. However, this kind of information is limited because of the small sample size in both databases. A Genome-Wide Association Study has been conducted with 8,842 Korean subjects as a part of the Korea Association Resource (KARE) project. In an effort to build a publicly available browsing system for genome data resulted from large scale KARE GWAS, we developed the KARE browser. This browser provides users with a large amount of single nucleotide polymorphisms (SNPs) information comprising 1.5 million SNPs from population-based cohorts of 8,842 samples. KAREBrowser was based on the generic genome browser (GBrowse), a webbased application tool developed for users to navigate and visualize the genomic features and annotations in an interactive manner. All SNP information and related functions are available at the web site http://ksnp.cdc. go.kr/karebrowser/.     

Using genomic databases for sequence-based biological discovery

The inherent potential underlying the sequence data produced by the International Human Genome Sequencing Consortium and other systematic sequencing projects is, obviously, tremendous. As such, it becomes increasingly important that all biologists have the ability to navigate through and cull important information from key publicly available databases. The continued rapid rise in available sequence information, particularly as model organism data is generated at breakneck speed, also underscores the necessity for all biologists to learn how to effectively make their way through the expanding "sequence information space." This review discusses some of the more commonly used tools for sequence discovery; tools have been developed for the effective and efficient mining of sequence information. These include LocusLink, which provides a gene-centric view of sequence-based information, as well as the 3 major genome browsers: the National Center for Biotechnology Information Map Viewer, the University of California Santa Cruz Genome Browser, and the European Bioinformatics Institute's Ensembl system. An overview of the types of information available through each of these front-ends is given, as well as information on tutorials and other documentation intended to increase the reader's familiarity with these tools.     

GGVD: A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions

Understanding the evolutionary history and adaptive process depends on the knowledge that we can acquire from both ancient and modern genomic data. With the availability of a deluge of whole-genome sequencing data from ancient and modern goat samples, a user-friendly database making efficient reuse of these important resources is needed. Here, we use the genomes of 208 modern domestic goats, 24 bezoars, 46 wild ibexes, and 82 ancient goats to present a comprehensive goat genome variation database(GGVD). GGVD hosts a total of ～41.44 million SNPs, ～5.14 million indels, 6,193 selected loci, and 112 introgression regions. Users can freely visualize the frequency of genomic variations in geographical maps,selective sweeps in interactive tables, Manhattan plots, or line charts, as well as the heatmap patterns of the SNP genotype. Ancient data can be shown in haplotypes to track the state of genetic variants of selection and introgression events in the early, middle, and late stages. For facilitating access to sequence features, the UCSC Genome Browser, BLAT, BLAST, Lift Over, and pcadapt are also integrated into GGVD.GGVD will be a convenient tool for population genetic studies and molecular marker designing in goat breeding programs, and it is publicly available at http://animal.nwsuaf.edu.cn/Goat Var.     

The Organelle Genome Database Project (GOBASE).

The taxonomically broad organelle genome database (GOBASE) organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the mitochondrial subset of data and contains molecular sequences, RNA secondary structures and genetic maps, as well as taxonomic information for all eukaryotic species represented. The database has been designed so that complex biological queries, especially ones posed in a comparative genomics context, are supported. GOBASE has been implemented as a relational database with a web-based user interface (http://megasun.bch.umontreal.ca/gobase/gobas e.html ). Custom software tools have been written in house to assist in the population of the database, data validation, nomenclature standardization and front-end design. The database is fully operational and publicly accessible via the World Wide Web, allowing interactive browsing, sophisticated searching and easy downloading of data.