[Compress]
DNA Sequence Compression (Random) Example
> Compress: L.Allison, Computer Science, Monash University 4/1998
1 GGATATCACG TAGTCCCTAG CTCTTGGCGC TGGATGGGGC GGACGGAAGG
51 GAAACGACCG TTGAATTCCA AATTCGGTCG TATGGAAATA TTGCAATGGA 100
> order-0 Markov Model
> | 4.0 +
> | 3.5 b
> | 3.0 b
> . . ... . . . . . . . .. .. . . . | 2.5 b
>--....-.--..-.---..--.-..-----.--..-------.---..---...--.---..-....--.....---.--...--.......--...--.|- 2.0 b
>.. . . . .. . .. .... .. .. ... . . . .. . .. . .. | 1.5 b
> | 1.0 b
> | 0.5 b
> | 0.0 b
> compress: Sequence length=100, |Alphabet|=4, log2(|Alphabet|) =2.0000
> hypothesis: (H) =8.2 bits
> data: (D|H) =197.4 bits, =1.9742 b/ch
> total: (H)+(D|H) =205.6 bits, =2.0564 b/ch
> ran 00/01/21 from 15:33:36 to 15:33:36
> order-1 Markov Model
> | 4.0 +
> | 3.5 b
> | 3.0 b
>. .. . .. .. . . . . . . . . . . . .. | 2.5 b
>--.-.-.----.--.....--....-----.--.--------.---.----.----.-.--.-.--...----..---.--.---.---.-.-------.|- 2.0 b
> . . . . .. . .. ..... .. .. . .. .. . . . .. ... .. . ... ... . . .... | 1.5 b
> | 1.0 b
> | 0.5 b
> | 0.0 b
> compress: Sequence length=100, |Alphabet|=4, log2(|Alphabet|) =2.0000
> hypothesis: (H) =21.1 bits
> data: (D|H) =191.0 bits, =1.9097 b/ch
> total: (H)+(D|H) =212.1 bits, =2.1208 b/ch
> ran 00/01/21 from 15:33:36 to 15:33:36
> AED fwd approx repeats
> [Frequencies B:99.1 R:0.3 C:0.6 E:0.3 =:0.8 ~:0.1 i:0.0 d:0.0 tot:101.3]
> [Frequencies B:98.5 R:0.7 C:0.9 E:0.7 =:0.7 ~:0.4 i:0.3 d:0.3 tot:102.7]
> [Frequencies B:97.9 R:1.1 C:1.2 E:1.1 =:0.8 ~:0.6 i:0.6 d:0.6 tot:104.0]
> | 4.0 +
> | 3.5 b
> | 3.0 b
>. .. . .. .. . . . . . . . . . . . .. | 2.5 b
>--.-.-.----.--.....--....-----.--.--------.---.----.----.-.--.-.--...----..---.--.---.---.-.-------.|- 2.0 b
> . . . . .. . .. ..... .. .. . .. .. . . . .. ... .. . ... ... . . .... | 1.5 b
> | 1.0 b
> | 0.5 b
> | 0.0 b
> compress: Sequence length=100, |Alphabet|=4, log2(|Alphabet|) =2.0000
> hypothesis: (H) =31.6 bits
> data: (D|H) =191.1 bits, =1.9110 b/ch
> total: (H)+(D|H) =222.7 bits, =2.2269 b/ch
> ran 00/01/21 from 15:33:36 to 15:33:38
> --- end ---
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L.Allison, Computer Science and SWE, Monash University, Australia 3168
http://www.csse.monash.edu.au/~lloyd/tildeStrings/
Fri Jan 21 15:33:38 EST 2000