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In contrast to the formal network representations of sequence similarity represented by previous studies describing algorithms for network generation, we have shown how well the displayed relationships reflect various measures of sequence and evolutionary distance, using relevant examples and quantitative assessments.
Protein similarity networks are graphical representations of sequence, structural and other similarities among proteins for which pairwise all-by-all similarity connections have been calculated.
A recent line of work (e.g. Daniels et al., 2013; Janin et al., 2014; Loh et al., 2012) aims at producing searchable, compressed representations of sequence information.
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Sparse representations of sequences facilitate signal processing tasks in many radar, sonar, communications, and information hiding applications.
Unlike categories, which are defining and therefore static representations, scripts are dynamic representations of sequences of behaviors associated with a particular context (Abelson 1976; Schank and Abelson 1977).
The z-domain representations of sequences x(k) and x*(k) are denoted as X[z] and X*[z*], respectively, where superscript * denotes complex conjugation.
However, manual, visually guided assembly of representations of sequence-based parts is unlikely to be scalable for large-scale computational design, especially where the detailed structure of the system to be designed is poorly understood.
We will continue to provide the definitive reference genome sequence for S. cerevisiae as well as variant sequences from these other sequenced strains, and are moving increasingly toward the representation of sequence variation and allelic differences.
Figure 2 Schematic representation of sequence alignment for the GBSSI alleles.
Sequence logos are a graphical representation of sequence alignments first developed by Schneider and Stephens [24].
The DRIM software package [40] was used to search for over-representation of sequence motifs in this set of sequences.
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