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Fig. 1 | BMC Bioinformatics

Fig. 1

From: DensityMap: a genome viewer for illustrating the densities of features

Fig. 1

Density map of genes, exons, ncRNA and GC % in chromosomes of D. melanogater. The command line was: DensityMap.pl -i dmel.gff3 -o egn -ty ‘gene = fused;exon = fused;ncRNA = fused = 10’ -gc 12 -sc 40000 -ba white -str_s 15 -str_w 25 -sp 35 -sh 50 -title “Density Map of Gene, Exon, ncRNA and GC%” -la −15 -ro ceil. The arms of chromosomes 2 and 3 are split into two annotation files 2 L, 2R and 3 L, 3R. Four density map were drawn for each chromosome, one each for genes, exons, ncRNA and GC%. Tilling windows were 40,000 bp long. Densities are represented with three colour scales. That for genes and exons is blue - red with colour tone changes for each 10 % density change. The second, for ncRNA, shows 0 % density as grey, densities of 1 to 9 % are represented by a blue—red colour gradient, and densities of 10 %l or greater by dark red. The third colour scale, for GC content, shows densities below 30 % in grey, 30–49 % as a green—red colour gradient, and densities of 50 % and above in dark red. The scale is in Mbp

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