CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6AFA_1 6TON_1 8HKH_1 Letter Amino acid
5 6 7 M Methionine
9 3 19 P Proline
7 9 14 R Arginine
6 7 38 N Asparagine
9 8 24 D Aspartic acid
4 4 10 Q Glutamine
15 6 26 E Glutamic acid
16 4 37 K Lycine
8 7 30 T Threonine
19 10 27 V Valine
3 5 2 C Cysteine
3 7 31 F Phenylalanine
24 8 19 A Alanine
18 5 28 G Glycine
10 9 29 I Isoleucine
9 9 23 S Serine
0 0 2 W Tryptophan
3 3 12 H Histidine
18 15 35 L Leucine
3 3 23 Y Tyrosine 

6AFA_1|Chain A|Protein/nucleic acid deglycase DJ-1|Homo sapiens (9606)
>6TON_1|Chain A|B-cell lymphoma 6 protein|Homo sapiens (9606)
>8HKH_1|Chains A, B|BoNT/A|Clostridium botulinum (1491)
Protein code \(c\) LZ-complexity \(\mathrm{LZ}(w)\) Length \(n=|w|\) \(\frac{\mathrm{LZ}(w)}{n /\log_{20} n}\) \(p_w(1)\) \(p_w(2)\) \(p_w(3)\) Sequence \(w=f(c)\)
6AFA , Knot 86 189 0.79 38 124 182 
MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGGNLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKMMNGGHYTYSENRVEKDGLILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD
6TON , Knot 65 128 0.82 38 98 125 
GPGADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKASE
8HKH , Knot 174 436 0.80 40 214 402 
MKKHHHHHHGLVPRGSPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTG

Let \(P_w(n)\) be the set of distinct subwords (intervals) in a word \(w\). Let \(p_w(n)\) be the cardinality of \(P_w(n)\). Let \(f(c)\) be the sequence in FASTA with 4-symbol Protein Data Bank code \(c\).

\(|P_{f(6AFA_1)}(2) \setminus P_{f(6TON_1)}(2)|=81\), \(|P_{f(6TON_1)}(2) \setminus P_{f(6AFA_1)}(2)|=55\). Let \( Z_k(x,y)=|P_x(k)\setminus P_y(k)|+|P_y(k)\setminus P_x(k)| \) be a LZ76 style (set of subwords) Jaccard distance numerator for \(P(k)\).Hydrophobic-polar version of Sequence 1:110001111110110010011110110011101011111100110000011101010100100011001111111011100100011100110000000111111011101111001111001000111000110110000000010001111000111001011111101101001110101111100
Pair \(Z_2\) Length of longest common subsequence
6AFA_1,6TON_1 136 4
6AFA_1,8HKH_1 162 4
6TON_1,8HKH_1 188 3

Newick tree

 
[
	8HKH_1:93.39,
	[
		6AFA_1:68,6TON_1:68
	]:25.39
]

Let d be the Otu--Sayood distance d.
Let d1 be the Otu--Sayood distance d1. (This makes the 4TYN sequence AAAAAA a close match...)
A roughly speaking expected distance is \((0.85)(0.8)(\frac{317 }{\log_{20} 317}-\frac{128}{\log_{20}128})=58.3\)
Status Protein1 Protein2 d d1/2
Query variables 6AFA_1 6TON_1 72 61
Was not able to put for d
Was not able to put for d1

In notation analogous to [Theorem 16, Kjos-Hanssen, Niraula and Yoon (2022)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]