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Figure 4 | BMC Bioinformatics

Figure 4

From: Identifying elemental genomic track types and representing them uniformly

Figure 4

GTrack example files. A) GTrack version of the GFF file in Figure 3A. GTrack conversions of GFF vary according to the set of attributes present in the GFF file. The column selected as the main value may also be changed. B1 and B2) Two possible GTrack conversions of the BED file in Figure 3B. In the direct variant (B1) only a "track type" header line and a column specification line are added. The exon positioning will in this case not be understood by a general GTrack parser. The linked variant (B2) expands the exons into subsegments that links to their parent gene segment. C1 and C2) GTrack conversions of the WIG files in Figure 3C. The variableStep file has sparse track elements covering single base pairs, with associated values. The track is thus of type valued points. The fixedStep file contains dense data, with the same values for a series of consecutive base pairs. The track type is thus of type step function. Note that in the last example, the end values are used for positioning. D) Example GTrack file of type linked genome partition. Here two graphs are defined, one directed and one undirected. To change the active graph, the edges column in the column specification line needs to be changed, in addition to the "undirected edges" header line. The example GTrack files are available at [20]. BioXSD 1.1 versions of the examples are available as follows: A [21], B1 & B2 [22], C1 [23], C2 [24], and D [25].

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