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

[Gilles HUNAULT]

Thank you for your quick reply. Several hundreds of state are fine
for the data that we want to analyze. I will try the functions of
TraMiner and tell you what we get...

<<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/

Le 23/02/11 à 10:09 (+0100), Alexis Gabadinho a écrit :

> 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!
>
> Salutations,
> Alexis.
>
>
> 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/
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