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Protomata-Learner version 0.07 ( warning : Beta version )



Protomata-Learner documentation

Examples data



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Partial Local Multiple Alignements (PLMA)


Sequences


Advice : reduce the redundancy in your set of sequences, for example use the program decrease redundancy at Expasy.

Upload your sequences file (FASTA)

Or paste your sequences











Sequence type : Proteins    DNA     DNA (with coding regions)  

Paloma parameters


Fragments similarity threshold

Consensus

Minimum fragments size

Maximal fragments size

OR

Import a PLMA file


PLMA file   

Protomaton

Quorum
(minimum number of sequences per block)
default 3/3, 2/3, 1/3 of the sequences     user defined quorum list (separated by commas)



Advanced parameters :

  Identification and generalization of position wrt physico-chemical properties

Use predefined amino-acid group           or user defined  

Likelihood thresholds for generalization (1 : no generalization, 0 : forced generalization)

   to a group , g : 

   to a wilcard (when a generalization to group failed) , s : 

Data examples







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