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rmes.gaussien
Gaussian Approximation of Word Counts |
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Description | Usage | Options | Sequence file | Output file | Examples |
rmes.gaussien [-english] -hor
rmes.gaussien -o <prefix> -seq DNA-sequence-file [-phase] [-m <m> | -max] [ [-hmin <hmin>] [-hmax <hmax>] | -fam family-file ] [-mart [-rev] ] [-english]
Examples
rmes.gaussien -o lambda.gaussien.3_1 -seq lambda -hmin 3 -m 1 rmes.gaussien -o pt7.gaussien.3_1 -seq pt7 -hmin 3 -m 12- Computation of the statistics of the phased 4-words in a coding DNA sequence of E. coli (coli-codant) under M2_3. Four output files coli-codant.gaussien.4_2.1, .2, .3 and .4 are then created corresponding to the words in phase 1, 2, 3 and all phases together.
rmes.gaussien -o coli-codant.gaussien.4_2 -seq coli-codant -hmin 4 -m 2 -phase3- Computation of the statistics of the 4-words in the ecomori sequence under M1 and then under M2. The output files ecomori.gaussien.4_1.0 and ecomori.gaussien.4_2.0 are then created.
rmes.gaussien -o ecomori.gaussien.4_1 -seq ecomori -hmin 4 -m 1 rmes.gaussien -o ecomori.gaussien.4_2 -seq ecomori -hmin 4 -m 24- Computation of the statistics of the 3-words, 4-words, 5-words and 6-words in the ecomori sequence under maximal models. We chose the Mart algorithm. The output file ecomori.gaussien.mart.3-6_max.0 is then created.
rmes.gaussien -o ecomori.gaussien.mart.3-6_max -seq ecomori -hmin 3 -hmax 6 -max -mart5- Computation of the statistics of the phased 4-words, 5-words and 6-words in a coding DNA sequence of E. coli (coli-codant) under M2_3. Four output files coli-codant.gaussien.4-6_2.1, .2, .3 and .4 are then created corresponding to the words in phase 1, 2, 3 and all phases together.
rmes.gaussien -o coli-codant.gaussien.4-6_2 -seq coli-codant -hmin 4 -hmax 6 -m 2 -phase6- Computation of the statistics of four families rny, rnr, ynr and yry (contained in the family file myfam) in the lambda genome under the model M1. The file lambda.gaussien.myfam_1.0 is created.
rmes.gaussien -o lambda.gaussien.myfam_1 -seq lambda -fam myfam -m 17- Computation of the statistics of families of words on the sequences hf-rep (the replication genome of H. Influenzae) and hf-rep-sans-uptake (the replication genome of H. Influenzae without the uptake sequence aagtgcggt and its complementary) under the model M1. The family file is fam.xnxxxxxx.
rmes.gaussien -o hf-rep.xnxxxxxx_1 -m 1 -fam fam.xnxxxxxx -seq hf-rep rmes.gaussien -o hf-rep-sans-uptake.xnxxxxxx_1 -m 1 -fam fam.xnxxxxxx -seq hf-rep-sans-uptake