$ gibbs Usage(sites sampler): gibbs file lengths [options] Usage(motif sampler): gibbs file lengths expect [options] lengths = [,]: lengths of elements for each type expect = [,]: expected number of elements for each type [,] = numbers for each element (e.g. "10,12,15" for 3 types) options: -C - prob. cutoff (0 < C <= 1) for near optimum sampling -c - number of cycles between shifts (sites sampler) or maximum number of cycles per run (motif sampler) -d - DON'T use fragmentation (i.e., column sampler) -f - create a scan output file (file.sn) -I - interactively specify #sites/sequence (sites sampler) (default: one site of each type per sequence) -L - set rapid convergence limit (higher = longer to converge) -m - set maximum number of cycles in each run (sites sampler) -n - use nucleic acid alphabet -o - use element order in probabilities (sites sampler) (each sequence must contain the same number of elements) -p - number of pseudo counts for product multinomial model -q - pseudo counts for ordering model (sites sampler) -R - set number of near-optimum readings taken -r - randomly shuffle input sequences -s - give seed for random number generator -t - maximum number of sampling runs -x - DON'T remove protein low complexity regions -w - output wilcoxon rank test information (motif sampler) -W - set fractional weight (0 to 1.0) on priors (motif sampler) lovelace$ lovelace$ more trna.tfa >TRNA1 , 80 bases, 8CAAD343 checksum. GGGGATGTAGCTCAGTGGTAGAGCGCATGCTTCGCATGTATGAGG CCCCGGGTTCGATCCCCGGCATCTCCA >TRNA2 , 80 bases, 211A9972 checksum. GCGGCCGTCGTCTAGTCTGGATTAGGACGCTGGCCTCCCAAGCCAGCAA TCCCGGGTTCGAATCCCGGCGGCCGCA >TRNA3 , 80 bases, 1FA08758 checksum. GGCCCTGTGGCTAGCTGGTCAAAGCGCCTGTCTAGTAAACAGGAGA TCCTGGGTTCGAATCCCAGCGGGGCCTCCA >TRNA4 , 80 bases, CB555AA6 checksum. GGGCGAATAGTGTCAGCGGGAGCACACCAGACTTGCAATCTGGTAG GGAGGGTTCGAGTCCCTCTTTGTCCACCA >TRNA5 , 80 bases, 76BDF6E2 checksum. GCCGGGATAGCTCAGTTGGTAGAGCAGAGGACTGAAAATCCTCGTG TCACCAGTTCAAATCTGGTTCCTGGCA >TRNA6 , 80 bases, 82C57DF6 checksum. GGGGCCTTAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGG TCAGCGGTCGACCCGCTAGGCTCCACCA >TRNA7 , 80 bases, 6CE4E09E checksum. GGGCACATGGCGCAGTTGGTAGCGCGCTTCCCTTGCAAGGAAGAGG TCATCGGTTCGATTCCGGTTGCGTCCA >TRNA8 , 80 bases, 60753A8C checksum. GGGCCCGTGGCCTAGTCTGGATACGGCACCGGCCTTCTAAGCCGGGGA TCGGGGGTTCAAATCCCTCCGGGTCCG >TRNA9 , 80 bases, 845D2EFF checksum. CGGCACGTAGCGCAGCCTGGTAGCGCACCGTCCTGGGGTTGCGGGGG TCGGAGGTTCAAATCCTCTCGTGCCGACCA >TRNA10 , 80 bases, 90DD3035 checksum. TCCGTCGTAGTCTAGGTGGTTAGGATACTCGGCTTTCACCCGAGAG ACCCGGGTTCAAGTCCCGGCGACGGAACCA lovelace$ gibbgs trna.tfa 8 bash: gibbgs: command not found lovelace$ gibbs trna.tfa 8 Invalid (non-negative) expected score: 0.787 using blast amino acid frequencies nconv = 500 ** 1 ** (new=9; old=4; w=9) 0.44898 motif A cycle 3 (new=10; old=6; w=10) 0.875 motif A cycle 5 5 (new=4; old=5; w=10) 3.5 motif A cycle 6 (new=5; old=8; w=10) 3.5 motif A cycle 7 (new=8; old=1; w=9) 44[+] motif A cycle 8 (new=10; old=7; w=10) 0.916667 motif A cycle 10 10 (new=5; old=6; w=10) 0.285714 motif A cycle 11 (new=7; old=8; w=10) 3.5 motif A cycle 12 (new=8; old=7; w=10) 3.5 motif A cycle 13 (new=11; old=8; w=11) 1 motif A cycle 14 (new=0; old=10; w=12) 0.4[-] motif A cycle 15 15 (new=14; old=12; w=14) 0.714286 motif A cycle 17 (new=9; old=2; w=14) 1 motif A cycle 18 (new=16; old=3; w=16) 0.967033 motif A cycle 19 ** 2 ** (new=9; old=3; w=9) 0.166667 motif A cycle 3 5 (new=3; old=8; w=9) 12.8333 motif A cycle 6 (new=8; old=4; w=9) 3.5 motif A cycle 7 (new=4; old=9; w=8) 7 motif A cycle 8 [++] 1 motif A cycle 8 (new=10; old=1; w=9) 2[+] motif A cycle 9 (new=8; old=5; w=9) 0.857143 motif A cycle 10 10 (new=10; old=8; w=10) 0.916667 motif A cycle 11 (new=8; old=4; w=10) 1 motif A cycle 13 ** 3 ** [+] 1 motif A cycle 3 (new=9; old=7; w=9) 0.5 motif A cycle 4 (new=7; old=9; w=8) 7 motif A cycle 5 [+] 1.16667 motif A cycle 5 5 (new=0; old=8; w=8) 1[-] motif A cycle 7 [-] 1 motif A cycle 7 (new=9; old=2; w=9) 1.57143 motif A cycle 8 (new=2; old=1; w=8) 7[+] motif A cycle 9 [++++] 1 motif A cycle 9 [-] 1 motif A cycle 10 [+] 0.857143 motif A cycle 11 [++++] 11.5238 motif A cycle 13 [+++] 9.87755 motif A cycle 14 [++] 0.857143 motif A cycle 15 15 (new=9; old=4; w=9) 0.44898 motif A cycle 17 ** 4 ** [--] 1.16667 motif A cycle 3 [++] 1 motif A cycle 4 [++] 1 motif A cycle 5 [+++] 3.66667 motif A cycle 6 [---] 1.16667 motif A cycle 7 [-] 0.758621 motif A cycle 8 [+++] 7.40816 motif A cycle 9 (new=9; old=1; w=8) 10.0833[+] motif A cycle 10 [++++] 417.366 motif A cycle 10 10 (new=9; old=1; w=8) 1[+] motif A cycle 11 [+] 1 motif A cycle 11 [++++] 108.653 motif A cycle 12 [++] 1 motif A cycle 13 [++] 3.14286 motif A cycle 15 15 (new=9; old=1; w=8) 34.5714[+] motif A cycle 16 [+++] 398.395 motif A cycle 16 [++++] 398.395 motif A cycle 17 (new=0; old=6; w=9) 0.142857[-] motif A cycle 19 (new=10; old=8; w=10) 0.25 motif A cycle 20 20 (new=7; old=2; w=10) 1 motif A cycle 21 (new=11; old=7; w=11) 1.16667 motif A cycle 22 (new=8; old=4; w=11) 0.333333 motif A cycle 23 (new=13; old=6; w=13) 2 motif A cycle 24 (new=4; old=9; w=13) 0.857143 motif A cycle 25 25 (new=14; old=4; w=14) 1.83333 motif A cycle 26 (new=12; old=3; w=14) 3.66667 motif A cycle 27 (new=15; old=11; w=15) 1.97436 motif A cycle 28 (new=3; old=8; w=15) 0.318182 motif A cycle 29 best = 111.882; oldbest = 111.882 MOTIF A 1-1 28 gtagagcgca TGCTTCGCA tgtatgaggc 36 2-1 46 tcccaagcca GCAATCCCG ggttcgaatc 54 3-1 1 GGCCCTGTG gctagctggt 9 4-1 46 caatctggta GGGAGGGTT cgagtccctc 54 5-1 47 aatcctcgtg TCACCAGTT caaatctggt 55 6-1 15 ccttagctca GCTGGGAGA gcgcctgctt 23 7-1 56 gtcatcggtt CGATTCCGG ttgcgtcca 64 8-1 56 ggatcggggg TTCAAATCC ctccgggtcc 64 9-1 51 gcgggggtcg GAGGTTCAA atcctctcgt 59 10-1 15 tcgtagtcta GGTGGTTAG gatactcggc 23 sites: * ******* 5 (10 sites in 10 sequences) Motif model (residue frequency x 100): POS C G A S T N D E Q K R H W Y F V I L M P Info 1 . . . . . . . . . . . . . . . . . . . . 0.0 3 . . . . . . . . . . . . . . . . . . . . 0.0 4 . . . . . . . . . . . . . . . . . . . . 0.0 5 . . . . . . . . . . . . . . . . . . . . 0.0 6 . . . . . . . . . . . . . . . . . . . . 0.0 7 . . . . . . . . . . . . . . . . . . . . 0.0 8 . . . . . . . . . . . . . . . . . . . . 0.0 9 . . . . . . . . . . . . . . . . . . . . 0.0 non- site . . . . . . . . . . . . . . . . . . . . site . . . . . . . . . . . . . . . . . . . . 8 columns Information (relative entropy) contribution in tenth bits: POS C G A S T N D E Q K R H W Y F V I L M P Info 1 . . . . . . . . . . . . . . . . . . . . 0 3 . . . . . . . . . . . . . . . . . . . . 0 4 . . . . . . . . . . . . . . . . . . . . 0 5 . . . . . . . . . . . . . . . . . . . . 0 6 . . . . . . . . . . . . . . . . . . . . 0 7 . . . . . . . . . . . . . . . . . . . . 0 8 . . . . . . . . . . . . . . . . . . . . 0 9 . . . . . . . . . . . . . . . . . . . . 0 site . . . . . . . . . . . . . . . . . . . . 0 Complete log-likelihood ratio = 111 bits Missing position information = 2 bits Log-likelihood ratio statistic = 108 bits Degrees of freedom = 152 Information per parameter = 0.717 bits MOTIF A 1-1 28 gtagagcgca TGCTTCGCA tgtatgaggc 36 (1.25) 2-1 46 tcccaagcca GCAATCCCG ggttcgaatc 54 (1.25) 3-1 1 GGCCCTGTG gctagctggt 9 (1.25) 4-1 46 caatctggta GGGAGGGTT cgagtccctc 54 (1.25) 5-1 47 aatcctcgtg TCACCAGTT caaatctggt 55 (1.25) 6-1 15 ccttagctca GCTGGGAGA gcgcctgctt 23 (1.25) 7-1 56 gtcatcggtt CGATTCCGG ttgcgtcca 64 (1.25) 8-1 56 ggatcggggg TTCAAATCC ctccgggtcc 64 (1.25) 9-1 51 gcgggggtcg GAGGTTCAA atcctctcgt 59 (1.25) 10-1 15 tcgtagtcta GGTGGTTAG gatactcggc 23 (1.25) sites: * ******* 5 (10 sites in 10 sequences) Motif model (residue frequency x 100): POS C G A S T N D E Q K R H W Y F V I L M P Info 1 . . . . . . . . . . . . . . . . . . . . 0.0 3 . . . . . . . . . . . . . . . . . . . . 0.0 4 . . . . . . . . . . . . . . . . . . . . 0.0 5 . . . . . . . . . . . . . . . . . . . . 0.0 6 . . . . . . . . . . . . . . . . . . . . 0.0 7 . . . . . . . . . . . . . . . . . . . . 0.0 8 . . . . . . . . . . . . . . . . . . . . 0.0 9 . . . . . . . . . . . . . . . . . . . . 0.0 non- site . . . . . . . . . . . . . . . . . . . . site . . . . . . . . . . . . . . . . . . . . 8 columns Information (relative entropy) contribution in tenth bits: POS C G A S T N D E Q K R H W Y F V I L M P Info 1 . . . . . . . . . . . . . . . . . . . . 0 3 . . . . . . . . . . . . . . . . . . . . 0 4 . . . . . . . . . . . . . . . . . . . . 0 5 . . . . . . . . . . . . . . . . . . . . 0 6 . . . . . . . . . . . . . . . . . . . . 0 7 . . . . . . . . . . . . . . . . . . . . 0 8 . . . . . . . . . . . . . . . . . . . . 0 9 . . . . . . . . . . . . . . . . . . . . 0 site . . . . . . . . . . . . . . . . . . . . 0 seed 425718694 time: 1 seconds (0.02 minutes)