Frequently asked questions

Thanks for taking the time to read these FAQs! We really appreciate it. We're working hard to make DNAlive a useful tool but, unfortunately, our tests cannot cover all issues. Suggestions and bug reports can be sent to the webmaster and we will do our best to track them.

If your question is not answered here, please contact us.

Index


General

Page requirements

To use DNAlive you only need a web browser. Please update your browser to the lastest version! For Internet Explorer, that is version 7 or higher and, for Firefox, please use version 2 or higher

Some scripts in our page won't work with Firefox version 1 or Internet Explorer versions 5 or 6. If you use other browsers, please refer to their documentation in order to get the lastest version.

To view Java applets, you will need the Java plug-in for your browser

How do I get feedback about the status of my processes?

Look for information messages at the bottom of the page or next to the button you just pressed. If something goes wrong, an error message will appear, and you are encouraged to report the bug to us by clicking on the link provided.

Can I use DNAlive with a non-human sequence?

DNAlive is 100% functional for any type of DNA sequence. Furthermore, if you are using any of the supported genomes, you will be able to use BLAT and the UCSC Genome Browser to view your sequence.

Which are the supported genomes?

As stated above, you can work with any DNA sequence, but more information is available for the following genomes:

The computing time of the physical properties is slow

Are you calculating Bubbles or Nucleosomes? Try disabling them. In general, the page reacts almost in real time, but please try unchecking removing some of the physical properties if you do not need them. Also, try using a smaller sequence, < 2000 base pairs for example.

The back/forward buttons of my browser don't work

This happens in most modern web sites. In DNAlive, you are not really browsing through different pages but the same page, only that it displays distinct information. That is why you can use our own back/next buttons at the bottom and the page responds instantly.

What is "BLAT"?

BLAT on DNA is designed to rapidly match 95% or even better similarity for sequences longer than 25 bases. It may miss more divergent or shorter sequence alignments, but it will find perfect sequence matches of 25 bases, and sometimes find them down to 20 bases.

BLAT on proteins matches 80% and better similarity for proteins larger than 20 amino acids. DNA BLAT works well on primates, and protein BLAT on land vertebrates.

You will find more information about BLAT in James Kent (2002) BLAT - The BLAST-Like Alignment Tool, Genome Res 12:4 656-664 and http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign

What is a "FASTA" file?

In bioinformatics, the FASTA format is a text-based format for representing either nucleic acid sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences.

A sequence in FASTA format begins with a single-line description, followed by several lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. The word following the ">" symbol is the identifier of the sequence, and the rest of the line is the description (both are optional). There should be no space between the ">" and the first letter of the identifier. You are recommended to limit the text lines to a maximum of 80 characters. The sequence ends when another line starting with ">" appears; this indicates the beginning of another sequence.

Here you can download a simple example of one sequence in FASTA format

Privacy policy

DNAlive does not use encryption, so the data travels through the internet as any other information does. Please do not use DNAlive with private, confidential or sensitive information, as we cannot guarantee its safety.

In case of a server error, the user is presented an informative screen while the server builds a report with the error data. This information is used to track and solve the error, and it is then deleted.

We use a cookie to track first-time visitors and show them an informational window. No personal info is gathered.

Finally, we use Google Analytics to learn more about our users and improve the navigation of the site.


Physical properties

Will new physical properties be added?

Yes. We are planning on adding new properties for the new release of the page.

2D View

How does the 2D view really work?

Currently you have the following options:

  1. Use a supported Genome coordinates. This way, the properties will be printed on the UCSC Genome Browser.
  2. Upload or paste a FASTA file, leaving the coordinates blank. 2D graphs will be plot using our own software.
  3. Upload/paste a FASTA file, and then run a BLAT search. If you are satisfied with the BLAT results and click on one, it will be entered into the coordinates box, so it is like going back to option 1.

Why is it that when the Genome Browser map opens in the 2D menu, I cannot see the physical properties?

The UCSC Genome Browser uses cookies to remember your last viewing options. Also, when you visit the UCSC Genome Browser, the physical properties may still be available. For more information please visit the Genome Browser user guide


3D View

In the 3D menu it seems that some TFBS have been automatically found by the scanning algorithm. But later, when I submit an expanded sequence containing the same DNA segment, the results are not consistent. Is this a bug?

No, it is not. The binding site prediction algorithm is based on probabilistic scores (see Lenhard et al. Bioinformatics 2002) and depends on total sequence size and composition. Furthermore, the user is able to edit his/her own TFBS annotation list.

Why is the TFBS list of my DNA sequence empty?

An automatic scan of your DNA sequence using relaxed constraints is run and the input sequence may produce many targets. Unfortunately, a small percentage of the targets have a PDB structure containing the protein bound to a single DNA helix.

Why is it that the black window doesn't show the DNA?

Jmol is used to render 3D images. This software is a great powerful tool, but it is also very memory hungry with long sequences like those that DNAlive supports. If you know what you are doing, increase the Java VM memory for your browser. Otherwise, the problem generally solves itself by fully closing the internet browser and then opening it again if you fully close the internet browser and then open it again.

Painting DNA physical properties on the 3D view is slow

Yes, we are aware of this problem and are working on it. Painting is almost instant on sequences smaller than 1000 base pairs and can take up to one minute on larger sequences. It is also very processor-dependant, so the faster your machine, the faster the DNA will be painted.


Chromatin Dynamics

Why can't I see the dynamics on my browser for sequences larger than 100 base pairs?

The 3D rendering software that we use (Jmol) is quite limited and cannot handle movies that large. After generating the dynamics for a long sequence, you can download the movie into your computer and then open it with other software, like VMD or PyMol.

What to do with the file dynamic.xyz.tar.gz?

The file is a xyz coordinate data file, compressed with the standard .tar.gz format. UNIX (Linux, Mac) users can uncompress it by simply double-clicking the downloaded file. Windows users may need uncompressing software like the free utility 7-zip

After that, a file named dynamic.xyz will be generated. You can open it with molecular viewing software, like VMD