CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8FHC_1 3CQP_1 3BBU_1 Letter Amino acid
5 7 4 N Asparagine
10 3 3 Q Glutamine
28 10 12 E Glutamic acid
1 1 2 W Tryptophan
17 5 11 R Arginine
7 11 2 D Aspartic acid
12 8 1 H Histidine
29 9 11 L Leucine
7 11 9 K Lycine
3 0 2 M Methionine
11 4 1 F Phenylalanine
13 10 4 S Serine
10 8 7 T Threonine
9 0 3 Y Tyrosine
5 24 4 G Glycine
10 5 3 P Proline
24 10 14 A Alanine
5 4 0 C Cysteine
12 9 4 I Isoleucine
5 14 7 V Valine 

8FHC_1|Chains A, B|tRNA-(MS[2]IO[6]A)-hydroxylase|gamma proteobacterium HdN1 (83406)
>3CQP_1|Chains A, B, C, D|Superoxide dismutase [Cu-Zn]|Homo sapiens (9606)
>3BBU_1|Chain A|Heat Shock Protein 15|Escherichia coli (562)
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 \(w=f(c)\)
8FHC , Knot 98 223 0.79 40 140 207 
HHHHHHMSQELLAPIKAFLGCETPQSWLQFATQDIETLLIDHANCEKKAAATALNLLFRYVERKELLTNLSQLAREELLHFEQVCEYMENMGIPYKHVPSSRYASSLRKQVRNEEPYRLVDILIIGAFIEARSCERFAALAPLLETQPETQELARYYRFLLKSESRHFEDYLALATQYFPDTEADLHARIAEIRECERELIESEDTEFRFHSGSPAPALRAGI
3CQP , Knot 74 153 0.81 36 115 149 
ATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLRNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
3BBU , Knot 52 104 0.77 38 84 99 
PAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLYEETAESVEKREKMALARKLNALT

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 \(c\).

\(|P_{f(8FHC_1)}(2) \setminus P_{f(3CQP_1)}(2)|=92\), \(|P_{f(3CQP_1)}(2) \setminus P_{f(8FHC_1)}(2)|=67\). 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 1:0000001000111110111100010011011000100111001000001110110111001000011001001100011010010001001111000110000100100010000100110111111110100000111111110001000011000011100000010001111000110001010101101000000110000001010010111110111
Pair \(Z_2\) Length of longest common subsequence
8FHC_1,3CQP_1 159 3
8FHC_1,3BBU_1 150 4
3CQP_1,3BBU_1 133 2

Newick tree

 
[
	8FHC_1:80.55,
	[
		3BBU_1:66.5,3CQP_1:66.5
	]:14.05
]

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 \((0.85)(0.8)(\frac{376 }{\log_{20} 376}-\frac{153}{\log_{20}153})=67.2\)
Status Protein1 Protein2 d d1/2
Query variables 8FHC_1 3CQP_1 84 70.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]