AMBER Archive (2007)

Subject: Re: AMBER: DNA Helicoïdal Plots over time

From: Vitor Felix (vfelix_at_dq.ua.pt)
Date: Mon Mar 12 2007 - 06:51:12 CST


Nelson
Ve este site, talvez valha a pena

Vitor
Stéphane Téletchéa wrote:
> Dear colleagues,
>
> I've put on my web site a little tutorial and some programs to plot
> DNA parameters over time. The full description is available at :
> http://www.steletch.org/spip.php?article32
>
> I've tried to explain the whole process, but basically the main tool
> (dnaplots.pl) uses pre-filtered data extracted from individual Curves
> analysis for getting a full plot over time for the defined parameter.
> For instance, you'll easily get 23 pages of parameters using this
> procedure (namely alpha, beta, gamma, delta, ... but also intra and
> inter base paris parameters). The final plots are generated with
> XmGrace so it is easy to used in an interactive mode after the first
> shot to tweak parameters to your convenience.
>
> The script is written in perl and can be adjusted to get more
> parameters (most of the time, it is just as easy as adding a
> description in one list).
>
> This setup has been successfully used for more than 4 years by me and
> some colleagues so i tried to place a clear description of the working
> procedure on the web page for others to benefit from this work.
>
> Feel free to ask if you need further input, and try to look inside the
> scripts (as recommended on the web page) in case you'll have some
> doubts about parameters.
>
> Hoping this will help you analyse faster your DNA trajectories,
>
> Stéphane Téletchéa
>

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