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The GenBank file format How to store more than just sequence information? Share this post. Awesome 06 Jul, Visit the course. I like the way of learning used in this course such as nterviewing the professional person associated to the field and encouragement to interact with other learners in the comment I need more of this course 07 Jul, I have learnt In this article, you will become familiar with another bioinformatic file type — the GenBank file format.
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Run Circleator as before, passing it both the configuration file and the GenBank flat file and directing the output into a. We can modify the percent-GC graph to show more detail by decreasing the range accordingly, perhaps to or even We can also increase the height of the graph to show more detail, as in the following example configuration file:. By default Circleator draws each genomic sequence to scale, but the scale can be changed in order to show greater detail in regions of interest at the expense of having a figure that is no longer drawn to scale.
Circleator will automatically compress the scale for the rest of the figure to compensate for the change. The following two lines in the configuration file effect the change of scale:. The next several lines of the configuration file are identical to those from the previous example and then the final four lines add some color and labels to the expanded region:.
The first field in any line is mandatory and must be either the name of a predefined track or the keyword new otherwise as in this case. The second optional field assigns a name to the track, h1 in this case. Assigning a unique name is recommended so that other tracks may refer unambiguously to this one if needed. The final field specifies the track options, separated by commas.
The options in this line are:. The second line above uses the coords predefined track type, which draws a circle and labels it with coordinate positions. We already have a coords track in the configuration file, which draws a full circle and then places a label every 0.
Unlike the Haemophilus influenzae sequence, which is a single finished sequence, the Propionibacterium acnes sequence is a high-quality draft that comprises 17 separate scaffolds. Each of the 17 scaffold sequences is a separate GenBank entry, and we could download them as separate files, but the simplest approach is to download a single GenBank flat file that contains all 17 sequences and their associated annotation.
Recall that this 3-line configuration file displays the coordinate system labels and the gene features, and nothing else. Note that in this figure we have several gene-free regions, which did not appear in example 1. The reason for this is that we have 17 scaffolds and, by default, Circleator places a 20 kb gap between each pair of adjacent scaffolds or contigs.
Circleator has a couple of command-line options that affect the handling of multi-sequence input data. Sequences that are shorter than this will be excluded from the display. This is why both tracks are visible even though the opacity option was not used. This forces the two to overlap:. The rectangle glyph is a curved rectangle with both a border whose thickness is controlled by the stroke-width and also a filled interior.
The two color options color1 and color2 determine what color to draw the border lines and fill the interior:.
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