<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/35543?offset=580 https://bioinformaticsonline.com/bookmarks/view/38443/genoplotr-plot-gene-and-genome-maps-project Wed, 12 Dec 2018 08:33:41 -0600 https://bioinformaticsonline.com/bookmarks/view/38443/genoplotr-plot-gene-and-genome-maps-project <![CDATA[genoPlotR - plot gene and genome maps project!]]> genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files.

Features

  • Linear representation of several segments of DNA
  • Comparisons represented by areas between the segments (like Artemis, for example)
  • Reads from common formats: Genbank, EMBL, blast, Mauve, and from user-generated tab files
  • Plot several subsegments of the same segment on the same line, separated by a //
  • Automatic or manual placement of the segments on the plot
  • Add annotations to all the lines
  • Create smart, automatic annotations for genomes, based on gene names
  • Add a user-generated tree
  • Add a global scale or a scale to each line
  • Use user-defined graphical functions to represent genes

Address of the bookmark: http://genoplotr.r-forge.r-project.org/

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/38561/hawkeye-an-interactive-visual-analytics-tool-for-genome-assemblies Tue, 01 Jan 2019 11:56:17 -0600 https://bioinformaticsonline.com/bookmarks/view/38561/hawkeye-an-interactive-visual-analytics-tool-for-genome-assemblies <![CDATA[Hawkeye: an interactive visual analytics tool for genome assemblies]]> Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye.

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-3-r34

Address of the bookmark: http://amos.sourceforge.net/wiki/index.php?title=Hawkeye

]]> Abhimanyu Singh