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DNA Skyline: fonts to facilitate visual inspection of nucleic acid sequences
 
Letter to the Editor
Jonas Jarvius and Ulf Landegren
Uppsala University, Uppsala, Sweden
BioTechniques, Vol. 40, No. 6, June 2006, p. 740
Full Text (PDF)

In a time of explosive increase of genomic information, there is a need for improved DNA literacy. Despite the availability of computer programs to evaluate DNA and RNA sequences, the human eye can still play a vital role in sequence analysis for patterns and motifs. We describe a set of fonts that represent DNA sequences in an intuitive manner, suitable for teaching and for visual inspection of strand complementarity, conserved motifs, and oligonucleotide probes. Similar notations to aid visual inspection of nucleic acid sequences have been described earlier (1,2,3), but they typically require dedicated software in order to operate, thereby reducing their simplicity. The fonts we have developed represent nucleotides in a manner similar to musical notes, with each nucleotide extending to one of four levels (see Figure 1). Gs are placed on top, followed by As and Ts, with Cs at the lowest level. The two nucleotides that form base pairs via three hydrogen bonds, G and C, occupy the extreme positions, while A and T, held together by two hydrogen bonds, take up the innermost two. Consecutive nucleotides are connected by an arrow at the top level in all positions, displaying the 5′ to 3′ orientation. This GATC font is designed so that complementary sequences exhibit a precise fit, and a variant CTAG font is also provided to represent the complement of a selected sequence. The fonts have proven useful in our own work on DNA probe assays [e.g., involving padlock (4), selector (5), and proximity (6) probes]. Once installed on a computer by dragging the font files into the local font directory, DNA sequence information represented in any text/image software can be easily viewed in DNA Skyline by selecting one of the fonts. DNA Skyline is a TrueType font set, making this notation platform independent, simple to use, and compatible with most computer programs that use fonts. The fonts and a user guide can be downloaded at www.genpat.uu.se/Skyline.html.



Competing Interests Statement

The authors declare no competing interests.

References
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3.) Zimmerman, P.A., M.L. Spell, J. Rawls, and T.R. Unnasch. 1991. Transformation of DNA sequence data into geometric symbols. BioTechniques 11:50-52.

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5.) Dahl, F., M. Gullberg, J. Stenberg, U. Landegren, and M. Nilsson. 2005. Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments. Nucleic Acids Res. 33:e71.

6.) Fredriksson, S., M. Gullberg, J. Jarvius, C. Olsson, K. Pietras, S.M. Gustafsdottir, A. Ostman, and U. Landegren. 2002. Protein detection using proximity-dependent DNA ligation assays. Nat. Biotechnol. 20:473-477.