[Traminer-users] does it apply to amino acid sequences ?

Alexis Gabadinho Alexis.Gabadinho at unige.ch
Wed Feb 23 10:09:45 CET 2011

Dear Gilles,

I guess you can use many tools in the TraMineR package to analyse DNA 
sequences. At least you can try, we are very much interested in such 
application that could help us to improve the package.

I imagine that one important difference between social science and DNA 
sequences is their length. We usually use TraMineR with sequences having 
at most several hundred of states, and I guess that you will have to set 
a high graphical resolution if you want to use the tools for 
visualization of sequences containing several thousand of amino acids.

The tools for - pairwise - sequence alignment will work fine (however, 
you cannot visualize pairwise sequence alignments at this time, but we 
have a function under development for this purpose). Multiple sequence 
alignment is not available at this time.

You can also handle sequences that do not start at the same position by 
using missing values.

If you give a try to TraMineR, let us know!


Le 22. 02. 11 13:46, Gilles HUNAULT a écrit :
> Dear TraMineR users,
> It seems to me that the data and examples shown in the
> R package are more or less oriented toward social or economical data.
> Since amino acid sequences are sequences of categorical data
> (through amino acid #1 in the first sequence does not correspond
> necessarily to amino acid #1 in the other sequences), is it
> correct to use the methods and functions of TraMineR for the
> analysis of amino acid sequences.
> Has anyone already seen such an application ?
> Thank you for your help.
> <<Au plaisir de vous relire.>>
> (.=.)
> Gilles J. HUNAULT, gilles.hunault at univ-angers.fr
> "Science needs culture and feelings"
> http://www.info.univ-angers.fr/pub/gh/
> _______________________________________________
> Traminer-users mailing list
> Traminer-users at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/traminer-users 

More information about the Traminer-users mailing list