Dataset Information

Gene Graphics: a genomic neighborhood data visualization web application.

ABSTRACT: Summary:The examination of gene neighborhood is an integral part of comparative genomics but no tools to produce publication quality graphics of gene clusters are available. Gene Graphics is a straightforward web application for creating such visuals. Supported inputs include National Center for Biotechnology Information gene and protein identifiers with automatic fetching of neighboring information, GenBank files and data extracted from the SEED database. Gene representations can be customized for many parameters including gene and genome names, colors and sizes. Gene attributes can be copied and pasted for rapid and user-friendly customization of homologous genes between species. In addition to Portable Network Graphics and Scalable Vector Graphics, produced representations can be exported as Tagged Image File Format or Encapsulated PostScript, formats that are standard for publication. Hands-on tutorials with real life examples inspired from publications are available for training. Availability and implementation:Gene Graphics is freely available at https://katlabs.cc/genegraphics/ and source code is hosted at https://github.com/katlabs/genegraphics. Contact:katherinejh@ufl.edu or remizallot@ufl.edu. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Harrison KJ

PROVIDER: S-EPMC5905594 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Publications

Gene Graphics: a genomic neighborhood data visualization web application.

Harrison Katherine J KJ Crécy-Lagard Valérie de V Zallot Rémi R

Bioinformatics (Oxford, England) 20180401 8

<h4>Summary</h4>The examination of gene neighborhood is an integral part of comparative genomics but no tools to produce publication quality graphics of gene clusters are available. Gene Graphics is a straightforward web application for creating such visuals. Supported inputs include National Center for Biotechnology Information gene and protein identifiers with automatic fetching of neighboring information, GenBank files and data extracted from the SEED database. Gene representations can be cus ...[more]

PMID: 29228171

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Dataset Information

Gene Graphics: a genomic neighborhood data visualization web application.

Publications

Gene Graphics: a genomic neighborhood data visualization web application.

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