DNAlive

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Hello there!

As this is your first time with DNAlive, maybe you would like some help to get started. First of all, please disable your popup blocker so that we can open the windows with the results.

DNAlive is very easy to use. Just input the required information, and press the "Next" button at the bottom right of the page. The server will guide you through each step.

At the top of this page you will find plenty of help, should you need it. And, as time is golden, there are short videos which demo how to use the web page.

Please enjoy working with DNAlive.

Step 3: Select the physical properties

DNAlive components at the INB bioinformatics platform: INB Web Workflow Enactor & Manager

As UCSC Genome Browser stores previous information in Cookies, non-selected properties may be visible anyway.   Unusual DNA conformation Z-DNA ? A-DNA ? Triplex stability ? Quadruplex ? DNA disruption energy Base-pair stacking ? Duplex disruption free energy ? Duplex stability free energy ? Stacking energy ? DNA 3DNA structure B-DNA twist ? Curvature ? Direction wedge ? Protein DNA twist ? DNA propeller-twist ? DNA non-linear dynamics DNA Bubble formation ? Bubble size Moderate time consuming   DNA flexibility Bendability ? Bending stiffness ? Nucleosome preference ? Protein deformation ? DNA stability Denaturation ? Melting temperature ? Stability ? PARMBSC0 Helical force constants Rise ? Roll ? Shift ? Slide ? Tilt ? Twist ? Regulation parameters ProStar (ProStar web server) ? Nucleosome potential ? Moderate time consuming

Step 3: Select a physical property

DNAlive components at the INB bioinformatics platform: INB Web Workflow Enactor & Manager

Unusual DNA conformation Z-DNA ? A-DNA ? Triplex stability ? Quadruplex ? DNA disruption energy Base-pair stacking ? Duplex disruption free energy ? Duplex stability free energy ? Stacking energy ? DNA 3DNA structure B-DNA twist ? Curvature ? Direction wedge ? Protein DNA twist ? DNA propeller-twist ? DNA non-linear dynamics DNA Bubble formation ? Bubble size Moderate time consuming   DNA flexibility Bendability ? Bending stiffness ? Nucleosome preference ? Protein deformation ? DNA stability Denaturation ? Melting temperature ? Stability ? PARMBSC0 Helical force constants Rise ? Roll ? Shift ? Slide ? Tilt ? Twist ? Regulation parameters ProStar (ProStar web server) ? Nucleosome potential ? Moderate time consuming

Main help | Input help

Step 1: Input modes

Choose one: paste or upload a DNA sequence, or enter genomic coordinates.

DNA Sequence (will be plot in DNAlive) Paste a DNA sequence Upload a DNA sequence file from your computer ► Click here to perform a BLAT search You can also use Blat? to define the coordinates of the input sequence within a genome. For this, you need to the file first and then select a species Chicken (galGal3) Chimp (panTro2) Fugu (fr2) Human (hg18) Mouse (mm9) Opossum (monDom4) Rat (rn4) Tetraodon (tetNig1) Zebrafish (danRer5) Ready to upload

Genomic coordinates (will be plot in the UCSC Genome Browser) Sample: (hg18) chr19:54,187,500-54,189,500 <Upstream promoter region of the Glycogen Synthase 1 (GYS1) gene> Chicken (galGal3) Chimp (panTro2) Fugu (fr2) Human (hg18) Mouse (mm9) Opossum (monDom4) Rat (rn4) Tetraodon (tetNig1) Zebrafish (danRer5)

Step 2: Select a plot type

Plot help

No plot, only the numeric results ?
2D plot using DNAlive ?
3D plot ?
Chromatin dynamics ?

Run the dynamics for the bases number to of ? bps.
Receive an e-mail with the results?
Your address:

100 bps is the standard value and 5,000 bps is the maximum size that our server supports. For values higher than 100, the result can't be displayed in the Jmol applet and you will receive the results in your e-mail. (?)

The Dynamics animation will show in your browser

Check for bound proteins?

They will be automatically calculated on the next step, and you will be able to review them. Only available for the 3D and 4D plots, and only for Humans.

[Contact] © 2007-2008. Molecular Modelling & Bioinformatics Unit. IRBB-PCB & University of Barcelona

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