gff2aplot: Plotting sequence comparisons.

Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra -Centre de Regulació Genòmica, Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.
Bioinformatics (Impact Factor: 4.62). 01/2004; 19(18):2477-9. DOI: 10.1093/bioinformatics/btg334
Source: PubMed

ABSTRACT gff2aplot is a program to visualize the alignment of two sequences together with their annotations. Input for the program consists of single or multiple files in GFF-format which specify the alignment coordinates and annotation features of both sequences. Output is in PostScript format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis.
gff2aplot is freely available under the GNU software licence and can be downloaded from the address specified below.

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Available from: Josep Francesc Abril, Aug 14, 2015
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    • "Obviously, such formulation of the problem results in the requirement of local scale regulation (local zoom) for visualization of non-trivial tracks, similar to that used in the dot-plot method implementations described in [11] [30]. At present, the dot-plot method is a part of various packages used in the field of bioinformatics [1] [6] [12] [28] [30] [34], where, as a rule, it is possible to make comparisons for any distance scale. "
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    ABSTRACT: The authors propose a simple version of the dot-plot scheme to be used in the case when the distances between sequence elements may take more than two values. The method is applicable, in particular, to the case of the sequences of large-length windows when the sets of distance values are continuous. The proposed technique is simple to implement and the results can produce readable maps for further analysis. To illustrate its potentialities, the method has been applied to the comparison of genomic sequences. The asymmetry in the number of direct and reverse tracks for the Homo sapience genome has been discovered.
    Information Sciences 04/2011; DOI:10.1016/j.ins.2010.12.009 · 3.89 Impact Factor
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    • "One effective paradigm is the dot plot. Utilities based on this paradigm include Dotter (Sonnhammer and Durbin, 1995) and gff2aplot (Abril et al., 2003). Though dot plots are an excellent way of giving a high level overview of large, complex regions, they are less suited for close detail. "
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    ABSTRACT: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization perspectives. The perpendicular (dot plot) view provides a dot plot of genome alignments synchronized with a display of genome annotations along each axis. The parallel view displays two genome annotations horizontally, synchronized through a panel displaying local alignments as trapezoids. Users can zoom to any resolution, from whole chromosomes to individual bases. They can select, highlight and view detailed information from specific alignments and annotations. Combo is an organism agnostic and can import data from a variety of file formats. AVAILABILITY: Combo is integrated as part of the Argo Genome Browser which also provides single-genome browsing and editing capabilities. Argo is written in Java, runs on multiple platforms and is freely available for download at
    Bioinformatics 08/2006; 22(14):1782-3. DOI:10.1093/bioinformatics/btl193 · 4.62 Impact Factor
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    ABSTRACT: Thesis (M. Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004. Includes bibliographical references (p. 62-64). Propelled by advances in sequencing technology, the advent of the genomic era brings the challenge of managing and interpreting massive amount of genomic data. A number of single-genome browsers have been developed for data display. However, they are unsuitable for comparative analysis. We present a dynamic and interactive visualization tool called ComBo that allows users to quickly navigate sequences, browse their similarities in a dot plot format, display sequence annotations in feature maps, and compare annotations in corresponding regions. ComBo allows users to directly control the display. They can compare any two regions in the sequences at any resolution, from an entire chromosome down to the residue level. Users can also retrieve detailed information on any displayed sequence feature or alignment. ComBo can import data from the Calhoun annotation database or flat files. Developed in Java, ComBo has a flexible infrastructure allowing the easy addition of functionality in the future. by Tamara H. Yu. M.Eng.and S.B.
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