- Open Access
Using a color-coded ambigraphic nucleic acid notation to visualize conserved palindromic motifs within and across genomes
© Rozak and Rozak; licensee BioMed Central Ltd. 2014
- Received: 15 August 2013
- Accepted: 8 January 2014
- Published: 22 January 2014
Ambiscript 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.
We 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.
Juxtaposing 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.
The sequence logo, developed by Schneider and Stephens in 1990 (Figure 1C) is another frequently-used strategy for visualizing multiple sequence alignments. Schneider and Stephens’ system presents aligned sequences as a graph in which the four basic IUPAC characters (C, T, A, and G) are sized according to the relative probability of finding the corresponding nucleotide at a particular location and stacked to indicate the overall information content encoded by that position. Schneider and Stephen’s successful formula for constructing Sequence Logos was later augmented by Gorodkin et al., who accounted for nucleotide variation across the entire sequence set as well as the possibility of finding gaps in an alignment.
Unfortunately, as with IUPAC ambiguity characters, the original Ambiscript notation does not include provisions for encoding the probability of finding a particular nucleotide at a given position in a multiple sequence alignment. Consequently, valuable data is lost when displaying alignments using Ambiscript consensus sequences as well as with IUPAC ambiguity symbols.
Ambiscript Mosaic is a modified version of the Ambiscript notation that permits individual nucleic acid symbols to be represented with colors computed according to the frequencies at which the corresponding nucleotides can be found in each position of a multiple sequence alignment. As with traditional mosaics, where clusters of differently colored glass, ceramic, or stone pieces create a recognizable image when viewed at a distance, the color-coded notation helps users discern biologically-meaningful patterns in nucleic acid sequence alignments.
Ambiscript Mosaic allows users to visually represent and compare sequence polymorphisms in a manner similar to that of the Sequence Logo but requires significantly less space. Furthermore, the color-coded consensus sequences retain all the functional and analytic benefits of the original ambigraphic nucleic acid notation, making it easy to complement sequences and spot biologically relevant palindromes in multiple sequence alignments. The new script also includes a provision for representing gap characters in alignments.
It is important to note that Ambiscript Mosaic is not intended to compete with widely-available computer algorithms, which can quickly and efficiently identify palindromes and other biologically significant patterns in vast tracts of aligned and unaligned sequences. Rather, the graphic display was designed to help convey previously-obtained computational and experimental results in a manner that can be quickly grasped and understood by readers.
Ambiscript Mosaic alignments and consensus sequences can be generated using the online Adobe Flex® application discussed in this article. Unlike the original Ambiscript notation, Ambiscript Mosaic displays do not require installation of special computer fonts.
Each of the Ambiscript Mosaic sequence alignments presented in this paper were rendered using the Ambiscript Mosaic Alignment Tool (a web-based Adobe Flex® application found athttp://www.ambiscript.org), which accepts FASTA-formatted multiple sequence alignments via an internet browser and displays the data as Ambiscript Mosaic consensus sequences. The consensus sequences are rendered by applying the graphic algorithms described below. Both the application and source code are freely available for download from the web site under an open source MIT license. We encourage interested readers to contribute to the code or adapt it for their own use.
Ambiscript Mosaic consensus sequences are constructed by nesting rather than combining nucleotide symbols with figure-ground reversals. Our original Ambiscript notation provides written and printed symbol sets for flexible use. The DNA Bold font, which uses solid shapes to represent each of the different bases (Figure 2), is functionally suited for encoding information in shades and hues as proposed here. However, a simple design change is needed before the characters can be used to handle color coding.
The original Ambiscript font handled sequence ambiguities with a figure-ground color reversal of the thymine over the cytosine symbol and the adenine over the guanine symbol. This figure-ground color reversal was accomplished by superimposing a white symbol for thymine (a rounded arch) against a black symbol for cytosine (a pointed arch) or a white symbol for adenine (an inverted, rounded arch) over a black symbol for guanine (an inverted, pointed arch) as shown in the Ambiscript DNA Bold column of Figure 2. The Ambiscript Mosaic font, on the other hand, modifies the cytosine and guanine characters so that they have spaces carved out for nesting the smaller thymine and adenine characters. Therefore, in this new system, the possibility of finding a cytosine and thymine at a particular position is denoted by using the new symbol for a cytosine (a pointed arch with a hollowed-out base) and filling its base with the smaller symbol for a thymine (a rounded arch). It is similarly possible to combine inverted, pointed and rounded arches to represent the possibility of finding an adenine and a guanine at the specified location. See the Ambiscript Mosaic column in Figure 2 for examples of how this system is applied to the eleven ambiguity characters.
This new strategy for assembling ambiguity characters has two advantages. First, the open arch further aids the visual distinction between characters. Second, and more importantly, by avoiding the figure-ground reversal used in the original Ambiscript notation, it becomes possible for each of the compounded characters to be colored differently based on the chances of finding the corresponding nucleotide at a given sequence position.
Any graphical representation of complex data requires a degree of practice and familiarity on the part of the reader to effectively perceive and understand the data contained in the graphic. Sequence data rendered via Ambiscript Mosaic is no different in this respect. Nevertheless, we have endeavored throughout our development of the ambigraphic notation to minimize the learning curve for new users by designing symbols that reflect key biological attributes of the nucleotides, using compound characters to greatly simplify the construction of ambiguity characters, and providing a simple mnemonic to help readers remember the meanings of the four symbols.
A graphic in Figure 2 illustrates how, when the compounded Ambiscript Mosaic characters are read from top to bottom, the first letters of the nucleotide names form the sequence C-TAG. Thus, the meaning of the individual symbols and compounded ambiguity characters is easily recalled by applying the phonetic mnemonic, "sea tag", which in a top to bottom read, links the ambigraphic symbols to the initial letters of the scientific names of the represented nucleotides.
The symbols and principles of Ambiscript Mosaic are such that they can be efficiently described and understood by readers via compact captions and keys, which accompany figures and tables in published manuscripts.
The grey-scaled approach produces two important visual cues. First, the symbols for the most frequently-occurring nucleotides at each position stand out more than the other characters at that location. Second, when the sequence is viewed as a whole, those regions of the genome with less variation are highlighted with dark characters sharply contrasted against the white background. Conversely, those regions with very little sequence homology appear much lighter with lower probabilities of occurrence, and hence lighter shading, evenly distributed among all possible nucleotides. This strategy for shading symbols according to the prevalence of the corresponding nucleotide in multiple sequence alignments provides an intuitive and very effective method for drawing the eye to darker regions of high homology and can be used to efficiently convey genetic disorder in a grey-scaled graphic. Moreover, the white-to-black-coded Mosaic symbols remain compact, allowing multiple consensus sequences to be displayed in a tabular format. Figure 4B takes advantage of this feature by rendering multiple sequences in a progressive format, which shows the accumulation of sequence polymorphisms as each new sequence is added to the list. When the aligned sequences are arranged in order of decreasing homology, the progressive format makes it easier to see the point at which the homologies break down.
Adding hue and chroma further aids visual discrimination between conserved and variable regions. It is possible to increase color discrimination in displays that permit more colors than simple mixtures of black and white. This is accomplished by adding hue and chromatic (saturation) perception to luminance (light-to-dark) perception.
The perceptual psychologist, Colin Ware, has observed that greater color sequence discrimination is achieved when hue differences coincide with light-to-dark differences. Therefore, when selecting a color scale for display on computer monitors we looked for one that produced the broadest light-to-dark discrimination that concurs with a pure light primary on one end of the scale.
We also chose to put complementary colors on opposite ends of the scale so that the range would pass through a neutral grey. This allows us to adjust the scale so that the visually distinct neutral grey corresponds to the possibility of randomly finding a nucleotide in a particular location. Depending on the GC-content of the assayed genomes, there is approximately a 25% chance of finding any of the four nucleotides at each position in a randomly-generated sequence. Therefore, any nucleotide that has a 25% chance of occurrence in the displayed sequence alignment is rendered in neutral grey. If all four base symbols are rendered in a neutral grey then it signifies that the alignment lacks apparent consensus at that particular position. Our online application allows users to adjust the scale so that middle grey corresponds with the random distribution of nucleotides in the assayed genome.
Gorodkin’s implementation of Sequence Logo specifically distinguishes nucleotides that occur more or less than random chance by inverting those characters that have a less than random chance of occurrence. This distinction is automatically achieved in Ambiscript Mosaic chromatic scale by recognizing that blue-tinted characters have a greater-than-random occurrence while yellow-tinted characters exhibit a less-than-random occurrence.
When optimizing the color scale for a computer monitor, placing any two of the red, green, or blue LCD light primaries at either end of the scale produces the greatest range of hues between a primary and its complementary hue. However, because none of the three LCD primaries are complementary to one another, they will not produce a neutral grey when mixed in equal amounts. Therefore, one must choose from one of the three primary-derived complementary pairs: red/cyan, green/magenta, or blue/yellow.
As mentioned above, this choice is guided by Ware’s observation that maximum color sequence discrimination is achieved when hue differences coincide with light-to-dark differences. Blue appears to be the darkest of the three full-intensity additive (light) LCD primaries used for digital display because human color vision is least sensitive to this wavelength in the visible electromagnetic spectrum. Furthermore, the particular yellow that is LCD primary blue’s true complement is the lightest hue producible at maximum saturation.
Propitiously, and not accidentally, when Ambiscript Mosaic is rendered with cyan, magenta, yellow, and black (CMYK), process color inks commonly applied in printed publications, yellow is the lightest primary pigment used and its complementary blue, achieved by the mixture of 100% magenta and 100% cyan, will be the darkest of the mixture of any of two of the cyan, magenta or yellow inks.
In Figure 5C, we compare consensus sequence data for the HssRS DNA binding motif using the grey scale consensus and the yellow-to-blue scale consensus. In this figure, the absence of a symbol indicates that the corresponding nucleotide is not represented at this particular position of the alignment. With respect to the yellow-to-blue color scale, the lightest and brightest yellow, which tends to blend with the white background, encodes the lowest percentage of occurrences of the signified nucleotide at this position. A neutral middle grey represents 25% occurrences of the signified nucleotide and the darkest and maximum chroma blue, which contrasts most sharply with the white page, represents 100% occurrences of the signified nucleotide at this position.
The Flex application allows for users to select between grey-scales and hue-augmented color scales to encode sequence polymorphisms depending on their personal preferences and the limitations of the particular computer or printed display. However, other color schemes could be developed in future versions of the software, to allow the incorporation of other data sets. For example, Sequence Logo effectively encodes a sequence’s information content in the cumulative heights of the displayed IUPAC characters. It may be possible to render the same information content using a redesigned Ambiscript Mosaic color scale.
The design of our original Ambiscript notation and our subsequent development of Ambiscript Mosaic have been influenced by information design principles proposed by Edward R. Tufte; an understanding of visual semiotics distilled from the writings of Saussure, Pierce, Dunne, and Frank; legibility studies performed by Miles Tinker; and visual perception and cognition research applied by Colin Ware to information design.
The first of Tufte’s principles of graphical excellence is that "graphical excellence consists of complex ideas communicated with clarity, precision, and efficiency". While the presentations and viewings of genetic data frequently deal with enormous complexity, Tufte’s principles of clarity, precision, and efficiency are poorly served by the IUPAC system of using capital or lower-case Roman letters.
To begin with, the IUPAC notation employs the initial letters of the chemical names for the nucleotides, which if one is aware of the words’ etymologies, vaguely recall the historical source of the chemicals rather than their functional significance within DNA strands. For example, adenine is derived from the Greek word aden, which means "gland" and refers to the chemical’s derivation from the pancreas of an ox. Similarly, guanine refers to guano, Spanish for "dung", from which the chemical was first isolated. The root for cytosine comes from Greek kytos for "a hollow, receptacle, basket". Thymine comes from "thyme", a plant of the mint family, with origins in Greek thymon, possibly from thyein for "burn as a sacrifice," which would indicate the plant used as incense. While these origins are interesting and may have mnemonic value to chemists and geneticists, they do little to highlight the functional or structural significances of the nucleotides within a DNA strand.
In contrast, the use of lower-case "c", " t", "a", " g" provide more readily distinguished patterns because of the degree to which the top of the "t" and the descender of the "g" extend above and below the horizontal space created by the "x" height portions of the four letters (Figure 8). Unfortunately, other visual cues, which could facilitate the identification of meaningful genetic patterns, are missing. For example, the "c" for cytosine does not have an ascender stroke to match the descender stroke on the "g" representing guanine. If the "t" did not have an ascender, it would better serve as a complement for the "a" representing adenine.
Comparing three different settings of the same genetic sequence, one with upper-case Roman characters, another with lower-case Roman characters and a third with Ambiscript Mosaic, all within the same-sized space, should demonstrate the much-improved clarity achieved with the Ambiscript Mosaic notation (Figure 8). Here, sequences of stronger and weaker nucleotide bonds, as well as sequences of heavier verses lighter nucleotides, and their resulting patterns are clearly evident, making it easier to locate palindromes. In contrast to type faces such as Garamond, which has an "x" height of 39% of the font’s type size, and Helvetica, which has an "x" height that is 52% of the font’s type size, we deliberately chose to remove the "x" height from Ambiscript. This eliminates the risk of burying any important character features within a high-density "x" height region. Instead, distinctive visual features appear above the horizontal baseline as ascenders and below the baseline as descenders. Fortunately, this high degree of legibility is much easier to accomplish for the four DNA symbols, than for the 26 lowercase Roman letters.
Recent studies in perception and cognition enable more accurate discussion of the differences between processing symbolic and non-symbolic signs. Symbols are socially approved signs, as opposed to sensory representations, such as size differences and color variations that are non-symbolic signs. Researchers, such as Colin Ware, refer to these non-symbolic signs as "perceptual representations". In developing our original Ambiscript symbols, we employed perceptual representations as much as we could to avoid the arbitrary signifiers (such as the historically remote use of pictographs to represent articulatory sounds and the entomologically obscure names for nucleotides) that are often required to overcome limits in human perception. Our use of color-coding applies additional perceptual representation (non-symbolic signs) to our solution.
Another of Tufte’s principles is that "graphical excellence is nearly always multivariate". To meet this criterion, displayed data should enable the simultaneous observation and the analysis of more than one data variable. We believe that we have made significant progress towards this standard by reconfiguring the Ambiscript characters to allow color-coded representations of genetic variation among multiple sequence alignments.
The figure-ground reversals used in our original Ambiscript notation enabled us to give readers "the greatest number of ideas in the shortest time with the least ink in the smallest space". Consequently, a single 8 point, black-on-white, ambiguity symbol can convey the presence of two, three or four different nucleotides in this particular position for as many DNA sequences as are being compared. However, our original design for Ambiscript ambiguity characters did not permit us to represent the frequency of each of these different nucleotide bases in any single location, as would be highly useful for a number of DNA analyses.
Fortunately, by using nested, rather than silhouetted symbols to construct consensus sequences, we can visually represent distributions of nucleotide polymorphisms using colors and shadings so that viewers can more easily perceive these patterns. The loss here is that human perception does not permit legible Ambiguity Mosaic symbols as small as 8 point type. At such small sizes color-coding becomes very unreliable because of what Ware explains as the occurrence of small-field color tritanopia, the inability to distinguish colors that are different in the yellow-blue direction. Not only this, color print reproduction and resolution at such small type sizes is questionable. However, the tradeoff benefit is the significant increase of information gained by the color-coded symbols.
First, sequences rendered in Ambiscript Mosaic require only a fraction of the space generally used for Sequence Logo displays. Even at half the size presented here, Ambiscript Mosaic is still very readable, while at that further reduction, Sequence Logo is that much less legible. This becomes an important feature when the number or size of the reported consensus sequences increases. It also makes it possible to compare multiple consensus sequences in tables or lists similar to the examples found in Figure 6. While Sequence Logos can and have been rendered in more compact spaces, this cannot be accomplished without loosing resolution on less than highly conserved regions of the sequence. Ambiscript Mosaic does not entail this sacrifice. Nevertheless, Ambiscript Mosaic’s compactness comes at a cost. It is harder to visually extrapolate precise values from a color scale than from the height-modulated characters used in Sequence Logo.
The second advantage that Ambiscript Mosaic offers over Sequence Logo is that the notation provides a more visually and conceptually coherent and attractive solution. It avoids the typographically awkward distortions that occur with the excessive vertical stretching and shrinking of letter-forms used for Sequence Logo, which not only produces unattractive typography, but also renders illegible variations.
The third and most important advantage Ambiscript Mosaic offers users is that the inherent symmetries found in the ambigraphic notation allow the reader to rapidly spot palindromic patterns that are often obscured in the IUPAC-derived presentation. This new functionality is available via a simple application, which can be downloaded or accessed online via Adobe Flash®-capable internet browsers athttp://www.ambiscript.org.
Project name: Ambiscript Mosaic
Project home page:http://www.ambiscript.org
Operating system(s): Platform independent
Programming language: Adobe Flex®
Other requirements: An Adobe Flash®-enabled internet browser
License: MIT License
The strategies and code described in this article were developed by the authors without external funding or assistance. However, the work benefitted from the availability of various high quality open source resources that have emerged from the dedicated and frequently uncompensated work of many. Among these tools were the Inkscape graphics suite, the FlashDevelop programming environment, and the Subversion version control system.
- IUPAC-IUB commission on biochemical nomenclature (CBN). Abbreviations and symbols for nucleic acids, polynucleotides and their constituents. Recommendations. Eur J Biochem. 1970, 15: 203-208.View ArticleGoogle Scholar
- Nomenclature for incompletely specified bases in nucleic acid sequences. Recommendations 1984. Nomenclature committee of the international union of biochemistry (NC-IUB). Proc Natl Acad Sci USA. 1986, 83: 4-8.View ArticleGoogle Scholar
- Cowin JE, Jellis CH, Rickwood D: A new method of representing DNA sequences which combines ease of visual analysis with machine readability. Nucleic Acids Res. 1986, 14: 509-515.PubMed CentralPubMedView ArticleGoogle Scholar
- Jarvius J, Landegren U: DNA Skyline: fonts to facilitate visual inspection of nucleic acid sequences. Biotechniques. 2006, 40: 740-PubMedView ArticleGoogle Scholar
- Johnson AD: An extended IUPAC nomenclature code for polymorphic nucleic acids. Bioinformatics. 2010, 26: 1386-1389.PubMed CentralPubMedView ArticleGoogle Scholar
- Schneider TD, Stephens RM: Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990, 18: 6097-6100.PubMed CentralPubMedView ArticleGoogle Scholar
- Gorodkin J, Heyer LJ, Brunak S, Stormo GD: Displaying the information contents of structural RNA alignments: the structure logos. Comput Appl Biosci. 1997, 13: 583-586.PubMedGoogle Scholar
- Rozak DA: The practical and pedagogical advantages of an ambigraphic nucleic acid notation. Nucleosides Nucleotides Nucleic Acids. 2006, 25: 807-813.PubMedView ArticleGoogle Scholar
- Hofstadter DR: Metamagical Themas: Questioning the Essence of Mind and Patterns. 1985, New York: Basic BooksGoogle Scholar
- Rozak DA, Rozak AJ: Simplicity, function, and legibility in an enhanced ambigraphic nucleic acid notation. Biotechniques. 2008, 44: 811-813.PubMedView ArticleGoogle Scholar
- Stauff DL, Torres VJ, Skaar EP: Signaling and DNA-binding activities of the Staphylococcus aureus HssR-HssS two-component system required for heme sensing. J Biol Chem. 2007, 282: 26111-26121.PubMedView ArticleGoogle Scholar
- Ware C: Information Visualization: Perception for Design. 2004, San Fransisco, CA: Morgan Kaufmann PublishersGoogle Scholar
- Schneider TD, Stormo GD, Gold L, Ehrenfeucht A: Information content of binding sites on nucleotide sequences. J Mol Biol. 1986, 188: 415-431.PubMedView ArticleGoogle Scholar
- McGuire AM, Hughes JD, Church GM: Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 2000, 10: 744-757.PubMedView ArticleGoogle Scholar
- Tsou AM, Cai T, Liu Z, Zhu J, Kulkarni RV: Regulatory targets of quorum sensing in vibrio cholerae: evidence for two distinct HapR-binding motifs. Nucleic Acids Res. 2009, 37: 2747-2756.PubMed CentralPubMedView ArticleGoogle Scholar
- Tufte E: The Visual Display of Quantitative Information. 1983, Cheshire, CT: Graphic PressGoogle Scholar
- Tinker MA: The relative legibility of the letters, the digits, and of certain mathematical signs. J Gen Psychol. 1928, 1: 472-496.View ArticleGoogle Scholar
- Online etymology dictionary. [http://www.etymonline.com],
- Papp PP, Chattoraj DK, Schneider TD: Information analysis of sequences that bind the replication initiator RepA. J Mol Biol. 1993, 233: 219-230.PubMedView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.