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.
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
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.
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.
As stated above, you can work with any DNA sequence, but more information is available for the following genomes:
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.
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.
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
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
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.
Yes. We are planning on adding new properties for the new release of the page.
Currently you have the following options:
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.
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.
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.
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.
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.
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