cMap: the comparative genetic map viewer

cMap, a www comparative genetic map graphical utility, has a search capability and provides comparison of two genetic maps within or between species with dynamic links to data resources and text lists of the shared loci, running in a relational database environment. Currently, maps from three species (maize 'Zea mays L.', rice 'Oryza sativa L.', and sorghum 'Sorghum bicolor L.'), representing over 13,800 distinct loci, are available for comparison at http://www.agron.missouri.edu/cMapDB/cMap.html. AVAILABILITY: cMap source code is available without cost on request for non-commercial use.     

The SGN comparative map viewer

Motivation: With the rapid accumulation of genetic data fora multitude of different species, the availability of intuitivecomparative genomic tools becomes an important requirement forthe research community. Here we describe a web-based comparativeviewer for mapping data, including genetic, physical and cytologicalmaps, that is part of the SGN website (http://sgn.cornell.edu/)but that can also be installed and adapted for other websites.In addition to viewing and comparing different maps stored inthe SGN database, the viewer allows users to upload their ownmaps and compare them to other maps in the system. The vieweris implemented in object oriented Perl, with a simple extensibleinterface to write data adapters for other relational databaseschemas and flat file formats. Contact: lam87{at}cornell.edu Associate Editor: Alex Bateman     

GenoMap,a circular genome data viewer

A Tcl/Tk-based application called GenoMap is described, a viewer for genome-wide map of microarray expression data within a circular bacterial genome. An interactive interface facilitates easy identification of the expressed region. This software is also used for drawing genome-wide quantitative data.     

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation

Background

Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity.

Results

To overcome these limitations we extended the Apollo data adapter with a generic, configurable web service client that is able to retrieve annotation data in a GAME-XML-formatted string and pass it on to Apollo's internal input routine.

Conclusion

This Apollo web service adapter, Apollo2Go, simplifies the data exchange in distributed projects and aims to render the annotation process more comfortable. The Apollo2Go software is freely available from ftp://ftpmips.gsf.de/plants/apollo_webservice.     

Towards a Drosophila genome map.

A physical map of the genome of Drosophila melanogaster has been created using 965 yeast artificial chromosome (YAC) clones assigned to locations in the cytogenetic map by in situ hybridization with the polytene salivary gland chromosomes. Clones with insert sizes averaging about 200 kb, totaling 1.7 genome equivalents, have been mapped. More than 80% of the euchromatic genome is included in the mapped clones, and 75% of the euchromatic genome is included in 161 cytological contigs ranging in size up to 2.5 Mb (average size 510 kb). On the other hand, YAC coverage of the one-third of the genome constituting the heterochromatin is incomplete, and clones containing long tracts of highly repetitive simple satellite DNA sequences have not been recovered.     

INE: a rice genome database with an integrated map view

The Rice Genome Research Program (RGP) launched a large-scale rice genome sequencing in 1998 aimed at decoding all genetic information in rice. A new genome database called INE (INtegrated rice genome Explorer) has been developed in order to integrate all the genomic information that has been accumulated so far and to correlate these data with the genome sequence. A web interface based on Java applet provides a rapid viewing capability in the database. The first operational version of the database has been completed which includes a genetic map, a physical map using YAC (Yeast Artificial Chromosome) clones and PAC (P1-derived Artificial Chromosome) contigs. These maps are displayed graphically so that the positional relationships among the mapped markers on each chromosome can be easily resolved. INE incorporates the sequences and annotations of the PAC contig. A site on low quality information ensures that all submitted sequence data comply with the standard for accuracy. As a repository of rice genome sequence, INE will also serve as a common database of all sequence data obtained by collaborating members of the International Rice Genome Sequencing Project (IRGSP). The database can be accessed at http://www. dna.affrc.go.jp:82/giot/INE.html or its mirror site at http://www.staff.or.jp/giot/INE.html     

Geno viewer, a SAM/BAM viewer tool

The ever evolving Next Generation Sequencing technology is calling for new and innovative ways of data processing and visualization. Following a detailed survey of the current needs of researchers and service providers, the authors have developed GenoViewer: a highly user-friendly, easy-to-operate SAM/BAM viewer and aligner tool. GenoViewer enables fast and efficient NGS assembly browsing, analysis and read mapping. It is highly customized, making it suitable for a wide range of NGS related tasks. Due to its relatively simple architecture, it is easy to add specialised visualization functionalities, facilitating further customised data analysis. The software's source code is freely available; it is open for project and task-specific modifications. AVAILABILITY: The database is available for free at http://www.genoviewer.com/     

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context

Background  

Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal.     

primetv: a viewer for reconciled trees

Background  

Evolutionary processes, such as gene family evolution or parasite-host co-speciation, can often be viewed as a tree evolving inside another tree. Relating two given trees under such a constraint is known as reconciling them. Adequate software tools for generating illustrations of tree reconciliations are instrumental for presenting and communicating results and ideas regarding these phenomena. Available visualization tools have been limited to illustrations of the most parsimonious reconciliation. However, there exists a plethora of biologically relevant non-parsimonious reconciliations. Illustrations of these general reconciliations may not be achieved without manual editing.     

Towards a high-resolution map of the Plasmodium falciparum genome

Until recently very little was known about the genome of Plasmodium falciparum. The situation has changed considerably with the advent of pulsed field gradient electrophoresis and yeast artificial chromosome technologies. It should now be possible to generate a high-resolution map within a few years. Here, Tony Triglia, Thomas Wellems and David Kemp review current knowledge.     

Human cytomegalovirus genome: partial denaturation map and organization of genome sequences.

Contour-length measurements of both nondenatured and partially denatured DNA from purified extracellular human cytomegalovirus indicate that more than one size class of viral DNA is encapsidated. In addition to a size class averaging about 100 x 10(6) daltons, a much less abundant class of larger viral DNA molecules, 150 x 10(6) to 155 x 10(6) daltons, was extracted from purified extracellular virus. As predicted by melting-curve analysis, partial denaturation of human cytomegalovirus DNA generates denaturation maps showing distinctive adenine plus thymidine (A+T)-rich and guanine plus cytosine (G+C)-rich localizations. Alignment of partial denaturation maps of both 100 x 10(6)- and 150 x 10(6)- to 155 x 10(6)-dalton molecules from maximum overlap of common A+T- and G+C-rich zones clearly shows six unique zones contained in a length equal to the longest class, 150 x 10(6) to 155 x 10(6) daltons. However, various alignments of the smaller class of the molecules within the confines of the approximately 100 x 10(6)-dalton-length equivalent are nondistinctive. Of the six unique A+T- and G+C-rich zones, five are linked in a specific sequence and maintain the same relative orientation; these features indicate the absence of major inversions within these zones. The sixth unique zone may occur at either end of this five-zone series, but it was never found at both ends of the same molecule. Additionally, this terminal zone appears to undergo complete inversions at least at one end of the alignment, and perhaps at both. These data indicate that 150 x 10(6)- to 155 x 10(6)-dalton molecules comprise human cytomegalovirus-specific genetic information.     

Trev: a DNA trace editor and viewer

Trev is a DNA trace editor and viewer, which is available free for UNIX and Microsoft Windows platforms. It can read all the commonly used file formats, including the new, compact ZTR files.     

Status of the cattle genome map

During the last 30 years, the cattle genome map has been expanded from 4 genes linked on chromosome X to over 22,000 genes identified in the cattle genome sequence assembly. This progress has been achieved due to numerous projects on linkage and physical mapping of the cattle genome driven by its agricultural and scientific significance. Indeed, the high-resolution mapping and functional analysis of the genome led to the discovery of major quantitative trait loci (QTL) regions and several quantitative trait nucleotides (QTNs), as well as some disease genes in the cow population. In addition, a comparison of the cattle genome to the genomes of other mammals has revealed its unique features gained during the speciation and adaptation. With the development of non-expensive sequencing techniques, the analysis of the cattle genome will shift towards the identification of differences between breeds or individuals within breeds that account for the unique features of each breed. This approach holds promise for the development of effective tools for the marker assistant selection and disease diagnostics in cattle.     

Prospects for a complete molecular map of the human genome

Linkage maps are limited by the number of recombinations that can be scored in human pedigrees to a resolution of ca. 1 centimorgan (relative distance between genes on a chromosome having a crossover value of 1%) which is estimated to be about 10 megabases. Molecular maps can be formed at any resolution down to the base sequence. To complement the linkage approach, the most useful molecular map would be one that helped to locate disease loci, by using restriction fragment length polymorphisms (RFLPS) and accurate localization of recombinations, and which then helped to find candidate genes in this region, by providing the positions of coding sequences. This paper discusses the appropriate form and scale of such a map, how it can be produced with methods now available, and the most efficient strategy for building the map, based on present knowledge of the organization of the human genome.