gff2ps: visualizing genomic annotations

Josep F. Abril Roderic Guigo Summary: gff2ps is a program for visualizing annotations of genomic sequences. The program takes the annotated features on a genomic sequence in GFF format as input, and produces a visual output in PostScript. While it can be used in a very simple way, it also allows for a great degree of customization through a number of options and/or customization files. Availability: gff2ps is freely available at http:// www1. imim.es/ jabril/ GFFTOOLS/ GFF2PS.html Contact: Supplementary information: http:// www1.imim.es/ jabril/ GFFTOOLS/ GFF2PS.html - As genomic sequences accumulate, visualization tools are becoming essential for the analysis and interpretation of sequence data. Recently, a format has been proposed for specifying genes and other features associated with genomic sequences, the General Feature Format (GFF, proposed by Durbin and Haussler, http://www.sanger.ac.uk/ Software/GFF/). In GFF each feature on the genomic sequence is described in a single-line record that essentially specifies the type and position of the feature on the genomic sequence. A grouping field allows to define sets of features within the GFF file. A number of tools have already been developed to deal with GFF files (see also at GFF URL). We have developed a tool, gff2ps, which allows for visualization of GFF files. gff2ps is a program written in GNU awk (http://www.gnu.org/software/gawk/ gawk.html) and PostScript, running on UNIX platforms, that generates a PostScript file given a GFF file. The page description language PostScript is recognized as the current de facto industry standard for high-quality printing. PostScript provides both a printer-independent and a computer-system-independent means to describe integrated text and graphics, which can be put out on a variety of printers, plotters and workstation screens. The generation of PostScript output is very common in sequence analysis tools. Notably, we can cite the RSVP package by Searls (1993). To whom correspondence should be addressed. gff2ps plots the features from different sources specified on a GFF file in a number of parallel rows (the so-called tracks here) along the length of the output page(s) (see Figure 1 for examples). Actually these are virtual pages (the so-called blocks here) allowing for several blocks to be included in a single physical page, or for splitting a single block in a number of physical pages. Features can be plotted in a variety of colors and shapes and those grouped together can be visually linked in a number of ways. gff2ps allows for a substantial amount of customization through command line options, and configuration files. However, meaningful output in most cases, meaningful output can be obtained without the need of any customization, by simply calling gff2ps with the input GFF file. gff2ps assumes, by default, that the GFF file itself carries enough formatting information. The examples in the figure show the versatility of gff2ps. Additional examples can be found at the gff2ps web page, as well as a detailed User Manual. One of the main advantages of gff2ps is its ability to manage many physical page formats, including userdefined ones. This allows, for instance, the generation of poster size genomic maps. As an example, we used gff2ps to display at the ISMB99 meeting, the predictions submitted to the Genome Annotation Assessment Project (GASP1) (http://www.fruitfly.org/GASP1/). The GASP1 plot was generated on three B0 size posters from a GFF file of over 50 000 feature records. The program has also been used to obtain the poster figures of recent relevant papers in genomic research (Adams et al., 2000; Reese, 2000). We thank Moise`s Burset and Gens Parra (IMIM) for their useful comments, Richard Bruskiewich (Sanger Center) for his helpful hints on the GFF format, also Elena Casacuberta and Amparo Monfort (CSIC) for motivating us to develop this tool. This work is supported by a grant from Plan Nacional de I+D, BIO98-0443-C02-01, and from a fellowship to J.A. from the Instituto de Salud Carlos III, 99/9345. Fig. 1. Different views of the same input GFF file, using gff2ps with different configuration files and command-line options. The top two pages on the left were obtained using the default configuration (specifying only the number of pages, and output media size). By default, gff2ps makes a number of assumptions. Among others: (i) Features grouped from the GFF input file (ungrouped features are treated as a single element group) within the same source are plotted in the minimum number of tracks, guaranteeing that different groups do not overlap. (ii) The plot is fitted into a single block (assuming the length of the sequence to be the end of the most downstream feature), and the block is printed into a single physical page. (iii) Features for which the frame is specified are plotted using a two color code schema. The upstream half of the graphical element representing the frame of the feature and the d (...truncated)