CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1TOU_1 9MEA_1 7RJN_1 Letter Amino acid
2 8 10 Q Glutamine
9 27 6 E Glutamic acid
1 15 2 H Histidine
2 3 3 W Tryptophan
11 24 6 D Aspartic acid
10 37 2 G Glycine
8 23 7 I Isoleucine
4 12 8 M Methionine
6 16 5 F Phenylalanine
1 18 9 P Proline
17 35 7 V Valine
4 13 10 N Asparagine
14 26 12 K Lycine
2 12 7 Y Tyrosine
6 42 6 A Alanine
2 7 2 C Cysteine
5 45 8 L Leucine
9 24 5 S Serine
12 22 6 T Threonine
6 25 2 R Arginine 

1TOU_1|Chain A|Fatty acid-binding protein, adipocyte|Homo sapiens (9606)
>9MEA_1|Chains A, B, C, D|Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1|Trichomonas vaginalis G3 (412133)
>7RJN_1|Chains A, B|Bromodomain-containing protein 3|Homo sapiens (9606)
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 \(w=f(c)\)
1TOU , Knot 66 131 0.81 40 100 125 
CDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKNTEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVMKGVTSTRVYERA
9MEA , Knot 176 434 0.82 40 221 406 
MAHHHHHHMSTEAPVLGILCGGGPAPGLNGVIAGATLYALRLGWKVIGFMEGFKYLCTGDVDVVKAHTIDLTYDIVSRIHFQGGTIIQTSRANPRKSPELQENVRKCLRALKVRYFLTIGGDDTASSAVSVASGMNGNEISVISCPKTIDNDLPLPADQSTFGFHTARSLGMEIIRNLMVDSKSAPRWFLVEAMGRSAGHLALGMAEASGAHLCLIPEEFKQDEIEFEDVVELVEATILKRLAYGKNYGVCVLAEGLVSKMSKKALYKLFGNREPPTDPHGHILLDDAELARSLSEELLKRLGNLGIRITPKKIGYELRCADPVAFDAVYTRELGYGAIDAFLNGHSAALIVRENGQVKPVQFKDLLDPATGRVRTRLVDVTSQSFKVARVYMWRMSKKDYENKDLVARVAAAGKMTPEAFTEKFAHLTDVVVE
7RJN , Knot 64 123 0.83 40 109 121 
SMPEVSNPSKPGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEE

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 \(c\).

\(|P_{f(1TOU_1)}(2) \setminus P_{f(9MEA_1)}(2)|=30\), \(|P_{f(9MEA_1)}(2) \setminus P_{f(1TOU_1)}(2)|=151\). 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 1:00111101011000010001001111110001111101011101010110100000100001011110010010100001000101011111010010100001000000001110011011000010001
Pair \(Z_2\) Length of longest common subsequence
1TOU_1,9MEA_1 181 3
1TOU_1,7RJN_1 149 3
9MEA_1,7RJN_1 212 3

Newick tree

 
[
	9MEA_1:10.36,
	[
		1TOU_1:74.5,7RJN_1:74.5
	]:30.86
]

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 \((0.85)(0.8)(\frac{565 }{\log_{20} 565}-\frac{131}{\log_{20}131})=126.\)
Status Protein1 Protein2 d d1/2
Query variables 1TOU_1 9MEA_1 156 100.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]