UCSC 2D help video

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Not sure about how to choose between the UCSC Genome Browser and DNAlive's plot? Check Input Help

UCSC Genome Browser

The selected DNA physical properties are computed and plotted in a two-dimensional map for visual inspection. If the input sequence corresponds to the human genome, and therefore, its genomics coordinates are known, a new pop-up window opens to link with the UCSC Genome Browser. Visualization of the data in that environment allows the user to compare physical descriptors, such as genes, exons, conservations across the species, among others, with annotations from other public databases.

The figure below is produced when submitting the genomics coordinates of gene GYS1 promoter region. †The TSS of the gene has been predicted using only the DNA physical properties (see ProStar). †Helical force constants (rise, roll, shift, slide, tilt and tiwst) are also computed and plotted in the 2D genomic map. Among the DNA properties related to chromatin structure, we selected nucleosome preference occupancy, double helix stacking energy and stability, and target sequences for triple and quadruple helix formation.

Via the UCSC Genome Browser options, the user can enrich the 2D plot with other annotation information such as genes, conservation, transcription factor binding sites, etc.

DNAlive 2D help video

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DNAlive plot

The user may be interested in non-human sequences from other genomes or simply chimeras of interest. In this case, the coordinate entry in the main page will be empty (the user can always force this option) and the DNAlive web server will not open the UCSC Genome Browser. Instead, a new window with two-dimensional plots of selected physical properties will open.

Interpretation of the results

Both the UCSC plot and DNAlive plot show the value of the physical properties. However, the way in which this value is shown differs.

The plot given by DNAlive is the most intuitive, as it prints a histogram with the X axis as the length of the sequence and the Y axis as the value for each nucleotide.

In contrast, UCSC prints colour bars that have no Y axis. The intensity of the grayscale (black is more, white is less) indicates the value of the property, so a high bar in DNAlive is represented in black in the UCSC Browser.

See how they compare with each other: the black areas correspond to high values, and the white areas to low values.