Input help video

Here you can watch a help video (work safe, without sound). If you have trouble, click here to download it, or just scroll down for more information

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Input window help

The different input modes

You have many options here. You can copy & paste a FASTA sequence into the large box (1) or simply upload a FASTA file from your computer (2)

If you use (1) or (2), and you know that these data correspond to the Human Genome, you can Save the file and launch a Blat Search (3) to look for the coordinates. A new window will open, please let it work for some minutes, as the Blat Search always takes a while.

When the results are displayed, you can click on the score of any of them, and its coordinates will appear in the coordinates box (4)

Obviously, you can input the coordinates directly into their box (4), for example the sample ones.

The results of a Blat Search

Not sure whether to use hg coordinates or a FASTA? It is simple. If you input the coordinates, the 2D plot will be displayed in the UCSC Genome Browser. If you use a FASTA, the 2D plot will be displayed in DNAlive.

As the UCSC Genome Browser has a lot of information about the human genome, we use it as the first option when coordinates are available. Easy, right?

Note: This only affects the 2D plot. The 3D plot and the Chromatin Dynamics will always be displayed in DNAlive's server.

In this case, the UCSC Genome Browser will be used for the 2D plot

Please read the Sequence boundaries help to understand how the length of your sequence affects the calculus of the physical properties.