A new method of representing DNA sequences which combines ease of visual analysis with machine readability

Cowin, J.E.; Jellis, C.H.; Rickwood, D.

doi:10.1093/nar/14.1.509

Cited by 7 publications

(2 citation statements)

References 3 publications

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“…Consequently, biologists have explored various graphic devices to augment the display and analysis of genetic data. For example, one such schema represents the bases as dots on a musical stave [ 3 ] (Figure 1 A) and a second, more recent strategy displays nucleotides as a string of variably sized blocks [ 4 ] (Figure 1 B). Both techniques offer the advantage of highlighting sequence polymorphisms but do not support clear visualization of consensus sequences from multiple sequence alignments.…”

Section: Introductionmentioning

confidence: 99%

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Using a color-coded ambigraphic nucleic acid notation to visualize conserved palindromic motifs within and across genomes

Rozak¹,

Rozak

2014

BMC Genomics

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BackgroundAmbiscript is a graphically-designed nucleic acid notation that uses symbol symmetries to support sequence complementation, highlight biologically-relevant palindromes, and facilitate the analysis of consensus sequences. Although the original Ambiscript notation was designed to easily represent consensus sequences for multiple sequence alignments, the notation’s black-on-white ambiguity characters are unable to reflect the statistical distribution of nucleotides found at each position. We now propose a color-augmented ambigraphic notation to encode the frequency of positional polymorphisms in these consensus sequences.ResultsWe have implemented this color-coding approach by creating an Adobe Flash® application ( http://www.ambiscript.org) that shades and colors modified Ambiscript characters according to the prevalence of the encoded nucleotide at each position in the alignment. The resulting graphic helps viewers perceive biologically-relevant patterns in multiple sequence alignments by uniquely combining color, shading, and character symmetries to highlight palindromes and inverted repeats in conserved DNA motifs.ConclusionJuxtaposing an intuitive color scheme over the deliberate character symmetries of an ambigraphic nucleic acid notation yields a highly-functional nucleic acid notation that maximizes information content and successfully embodies key principles of graphic excellence put forth by the statistician and graphic design theorist, Edward Tufte.

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Section: Introductionmentioning

confidence: 99%

“… Various strategies have been developed for visualizing genetic sequences. For example, the notation proposed by Cowin et al [ 3 ] uses dots arranged like notes on a music stave to display genetic data (A) . Jarvius and Landegren’s DNA Skyline notation [ 4 ] represents nucleotides as differently sized blocks (B) .…”

Section: Introductionmentioning

confidence: 99%