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GSDS / Gene Structure Display Server

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Assists users in visualizing gene structure and annotated features. GSDS also processes coordinates for exons and coding DNA sequence (CDS) and supports conserved elements and binding sites. This software enables the customization of the shape, size and color of annotation features after their initial render via an integrated visual editor. User-specified phylogenetic tree can be added to the figure result to simplify the evolutionary analysis.

GATExplorer / Genomic and Transcriptomic Explorer

Obsolete
Contains a gene loci browser with nucleotide level mappings of oligo probes from expression microarrays. GATExplorer enables interactive exploration of gene loci, transcripts and exons of human, mouse and rat genomes. It allows vision of probes in their own genomic context, with associated non-coding or protein-coding transcripts. In order to analyze transcriptomic data in a genomic context, five major datasets are integrated to this database.

ProtAnnot

Enables fast, efficient visual analysis of the impact of alternative transcription on proteins by extending standard genome browser iconography, in which linked blocks represent transcript structures and block thickness indicate translated regions. ProtAnnot searches InterPro and displays profile matches (protein annotations) alongside gene models, exposing how alternative promoters, splicing, and 3' end processing add, remove, or remodel functional motifs. To draw attention to these effects, ProtAnnot color-codes exons by frame and displays a cityscape graphic summarizing exonic sequence at each position. These techniques make visual analysis of alternative transcripts faster and more convenient for biologists.

DiseaseConnect

Obsolete
A web server for analysis and visualization of a comprehensive knowledge on mechanism-based disease connectivity. DiseaseConnect integrates comprehensive omics and literature data, including a large amount of gene expression data, genome-wide association studies catalog, and text-mined knowledge, to discover disease-disease connectivity via common molecular mechanisms. Moreover, the clinical comorbidity data and a comprehensive compilation of known drug-disease relationships are additionally utilized for advancing the understanding of the disease landscape and for facilitating the mechanism-based development of new drug treatments.

FeatureStack

A Perl module for the automatic generation of multi-gene images. FeatureStack takes BioPerl-compliant gene or transcript features as input and renders them side by side using a user-defined BioPerl glyph. Output images can be generated in SVG or PNG format. FeatureStack comes with a new BioPerl glyph, decorated_gene, which can highlight protein features on top of gene models. Used in combination, FeatureStack and decorated_gene enable rapid and automated generation of annotation-rich images of stacked gene models that greatly facilitate evolutionary studies of related gene structures and gene families.

GPViz

A versatile Java-based software for dynamic gene-centered visualization of genomic regions and/or variants. User-defined data can be loaded in common formats as resulting from analysis workflows used in sequencing applications and studied in the context of the gene, the corresponding transcript isoforms, proteins and their domains or other protein features. Both the genomic regions and variants can be also defined interactively. Various gene filter options are provided to enable an intersection of variants, genomic regions and affected protein features.

Gene Graphics

Allows creation of publication quality representations of gene neighborhoods for comparative genomics purposes. Gene Graphics allows for visually appealing representations of physical gene neighborhoods. The software allows customization of the default layout: colors, fonts, and sizes. Moreover, positions of gene and genome names can be edited both individually and globally. Gene Graphics supports multiple genomes in a single view, allowing visualization of homologs. The images generated can be used for record keeping and publications.

GECA

A fast, user-friendly and freely-available tool for representing gene exon/intron organization and highlighting changes in gene structure among members of a gene family. It relies on protein alignment, completed with the identification of common introns in the corresponding genes using CIWOG. GECA produces a main graphical representation showing the resulting aligned set of gene structures, where exons are to scale. The important and original feature of GECA is that it combines these gene structures with a symbolic display highlighting sequence similarity between subsequent genes. It is worth noting that this combination of gene structure with the indications of similarities between related genes allows rapid identification of possible events of gain or loss of introns, or points to erroneous structural annotations. The output image is generated in a portable network graphics format which can be used for scientific publications.

Intervene

Provides an easy and automated interface for effective intersection and visualization of genomic region sets, thus facilitating their analysis and interpretation. Intervene contains three modules: venn to generate Venn diagrams of up-to 6 sets, upset to generate UpSet plots of more than 3 sets, and pairwise to compute and visualize intersections of genomic sets as clustered heatmap. It provides flexibility to the user to choose figure colors, label text, size, resolution, and type to make them publication standard.

FancyGene

Obsolete
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A fast and user-friendly web-based tool for producing images of one or more genes directly on the corresponding genomic locus. Starting from a variety of input formats, FancyGene rebuilds the basic components of a gene (UTRs, intron, exons). Once the initial representation is obtained, the user can superimpose additional features-such as protein domains and/or a variety of biological markers-in specific positions. FancyGene is extremely flexible allowing the user to change the resulting image dynamically, modifying colors and shapes and adding and/or removing objects. The output images are generated either in portable network graphics (PNG) or portable document format (PDF) formats and can be used for scientific presentations as well as for publications. The PDF format preserves editing capabilities, allowing picture modification using any vector graphics editor.