[Traminer-users] does it apply to amino acid sequences ?
gilles.hunault at univ-angers.fr
Wed Feb 23 16:17:11 CET 2011
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"
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!
> 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"
>> Traminer-users mailing list
>> Traminer-users at lists.r-forge.r-project.org
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