Visualization Tools: gff2ps and gff2aplot
We developed a graphical visualization tool, the gff2ps program (Abril and Guigó, 2000), to represent genomic annotations. This program outputs high quality genomic plots in PostScript format and can cope with sequences of any length, for instance, eukaryotic genomes. This tool was used to generate the gene maps for the Drosophila melanogaster (Adams et al. 2000) and human genome (Venter et al, 2001, the figure below showing a fragment).
|A snapshot from the human genome figure, appeared in Venter et al (2001), showing annotation of segments of chromosomes 12 and 13 (top and bottom tracks respectively). An electronic version of that figure is available at the web site of Science.|
We also provide a tool to visualize pair-wise alignments of genomic sequences along with their corresponding annotations, gff2aplot (Abril et al, 2003). See "Gene finding based on comparative genomics" section figure for an example. A new implementation, written in perl, is already available for this program (since
gff2aplot version 2).
- J.F. Abril, R. Guigó and T. Wiehe. "
gff2aplot: Plotting sequence comparisons." Bioinformatics 19(18):2477-2479 (2003) [Abstract] [HomePage]
- R.A. Holt et al (including J.F. Abril and R. Guigó). "The Genome Sequence of the Malaria Mosquito Anopheles gambiae." Science 298(5591):129-149 (2002) [Abstract] Foldout figure: "Annotation of the Anopheles gambiae Genome Sequence." [Link to this Figure on Science website] [1.5Mb gzipped PostScript file] [2.9Mb gzipped PDF file]
- J.C. Venter et al (including J.F. Abril and R. Guigó). "The Sequence of the Human Genome." Science 291(5507):1304-1351 (2001) [Abstract] Foldout figure: "Annotation of the Celera Human Genome Assembly." [Link to this Figure on Science website] [2.7Mb gzipped PostScript file] [10Mb gzipped PDF file]
- M.G. Reese, G. Hartzell, N.L. Harris, U. Ohler, J.F. Abril and S.E. Lewis. "Genome Annotation Assessment in Drosophila melanogaster." Genome Research 10(4):483-501 (2000) [Abstract] Foldout figure: "Drosophila Genome Annotation Assessment Project" [Link to this Poster from Genome Research website] [466Kb gzipped PostScript file] [2.2Mb gzipped PDF file]
- M.D. Adams et al (including J.F. Abril). "The Genome Sequence of Drosophila melanogaster." Science 287(5461):2185-2195 (2000) [Abstract] Foldout figure: "Coding Content of the Drosophila Genome." [Link to this Figure on Science website] [1.1Kb gzipped PostScript file] [1.7Mb gzipped PDF file]
- J.F. Abril and R. Guigó. "
gff2ps: visualizing genomic annotations." Bioinformatics 16(8):743-744 (2000) [Abstract] [HomePage]
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