CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6DBA_1 6CBP_1 8TOV_1 Letter Amino acid
4 0 4 W Tryptophan
4 2 4 C Cysteine
8 2 16 E Glutamic acid
4 5 15 I Isoleucine
16 1 9 S Serine
3 0 4 F Phenylalanine
10 0 15 V Valine
7 2 20 A Alanine
7 4 11 R Arginine
5 1 7 D Aspartic acid
8 1 6 H Histidine
1 2 18 P Proline
11 2 16 T Threonine
8 1 15 Q Glutamine
15 2 18 G Glycine
11 0 18 L Leucine
2 0 10 M Methionine
7 5 10 N Asparagine
5 0 11 K Lycine
6 0 4 Y Tyrosine 

6DBA_1|Chains A, B|nanobody VHH R303|Camelus dromedarius (9838)
>6CBP_1|Chain A[auth P]|Man9-V3 glycopeptide|Human immunodeficiency virus 1 (11676)
>8TOV_1|Chains A, B, C, D, E, F, G, H, I, J, K, L|Matrix protein p17|Human immunodeficiency virus 1 (11676)
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 \(w=f(c)\)
6DBA , Knot 69 142 0.80 40 105 134 
QVKLEESGGGSVQAGGSLRLSCAASGHTYSTYCMGWFRQVPGKEREGVARINVGGSSTWYADSVRDRFTISQDNAKNTVYLQMNSLKLEDTAIYYCTLHRFCNTWSLGTLNVWGQGTQVTVSSGSEQKLISEEDLNHHHHHH
6CBP , Knot 19 30 0.71 26 25 27 
EINCTRPNNNTRPGEIIGDIRQAHCNISRA
8TOV , Knot 106 231 0.83 40 158 223 
PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

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 \(c\).

\(|P_{f(6DBA_1)}(2) \setminus P_{f(6CBP_1)}(2)|=97\), \(|P_{f(6CBP_1)}(2) \setminus P_{f(6DBA_1)}(2)|=17\). 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 1:0101000111010111010100110100000001111001110000111010111000101001000101000010001010100101000110000100100010110101110100101001000011000010000000
Pair \(Z_2\) Length of longest common subsequence
6DBA_1,6CBP_1 114 2
6DBA_1,8TOV_1 157 3
6CBP_1,8TOV_1 157 4

Newick tree

 
[
	8TOV_1:84.45,
	[
		6DBA_1:57,6CBP_1:57
	]:27.45
]

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 \((0.85)(0.8)(\frac{172 }{\log_{20} 172}-\frac{30}{\log_{20}30})=50.1\)
Status Protein1 Protein2 d d1/2
Query variables 6DBA_1 6CBP_1 62 37
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]