Figure 4.

Nucleotide level alignment of gene structures. A) Representation of gene structures with aligned introns. Grey bars represent exons and coloured lines introns. Exons are drawn to scale, while introns are represented in a length independent way. Introns at the same position are drawn in the same colour. The output also accounts for alignment gaps, which are drawn with thin black lines. B) Representation of the gene structures at the nucleotide level. Exons and introns are scaled that both represent 50% of the width of the figure. Without scaling, the introns would dominate the schemes. Red and magenta lines represent introns and intron gaps, respectively. Intron gaps are placeholders to fill the space of shorter introns compared to the longest intron at that position up to the next exon. The thick bars denote sequence within exons (green, orange and coral bars) and gap positions within exons (smaller blue bars) that were inserted into the protein sequences to adjust the multiple sequence alignment. Different colours for exonic sequences have been introduced to emphasize particular aspects like exons, which are not interrupted by sequence alignment gaps or introns in any of the other sequences (green bars) and the last uninterrupted parts of exonic sequence before introns (orange bars). The last option is particularly useful to identify the ends of exonic sequence before very short introns, or to identify introns in very huge alignments. Coral bars denote all other exonic sequence. Light gray lines symbolize placeholders within exonic sequences that are interrupted by introns in other sequences. All placeholders and markers for alignment gaps are added to optically align the corresponding exonic sequences beneath each other. C) Section of the gene structure alignment of B) with respect to the multiple sequence alignment to highlight the exon and intron features.

Hammesfahr et al. BMC Bioinformatics 2013 14:77   doi:10.1186/1471-2105-14-77
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