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logiciels:drimm:help_problength [2014/11/28 15:51] (current) |
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+ | ====== Help PROBAlength ====== | ||
+ | |||
+ | This program is dedicated to the computation, at each position of the sequence of the probability of appearance of the word of size <word_size> who appears at this position according to a Drifting Markov Model (DMM). | ||
+ | |||
+ | ===== Description of parameters ===== | ||
+ | |||
+ | |||
+ | ** -w <word size>** Size of words. | ||
+ | |||
+ | ** -a <alphabet_file>** A file describing the alphabet to use. | ||
+ | |||
+ | ** -s <sequences_file>** A file containing sequences. One model for all sequences. | ||
+ | |||
+ | ** -out <basename>** Basename for all ouput files. | ||
+ | |||
+ | ** -SpM** Estimation by splines (global). | ||
+ | |||
+ | ** -Spl** Estimation by splines (basis functions). | ||
+ | |||
+ | ** -SpH** Estimation by splines (no basis functions). | ||
+ | |||
+ | ** -Poly** Estimation by polynom (stochastic matrices). | ||
+ | |||
+ | ** -PolyM** Estimation by polynom (no stochastic matrices). | ||
+ | |||
+ | ** [-pos <in> <out>]** Compute the probabilities of the word for positions in to out. | ||
+ | |||
+ | ** -cf <config_file>** DMM is given by the config_file. | ||
+ | |||
+ | ** -h ** Print this help. | ||
+ | |||
+ | ===== Examples ===== | ||
+ | |||
+ | <code> | ||
+ | PROBAlength -w 3 -a dna.alpha -s lambda.fa -out three -Poly -cf config.out | ||
+ | </code> |