CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3UFN_1 1JZA_1 3ZQT_1 Letter Amino acid
4 1 15 Q Glutamine
4 1 17 F Phenylalanine
9 3 6 T Threonine
5 1 11 D Aspartic acid
7 8 14 K Lycine
2 1 4 W Tryptophan
8 5 28 L Leucine
4 6 14 E Glutamic acid
13 9 10 G Glycine
1 0 8 H Histidine
2 0 13 M Methionine
7 4 12 P Proline
0 5 17 S Serine
4 0 14 R Arginine
4 4 11 N Asparagine
0 8 6 C Cysteine
9 0 16 I Isoleucine
1 6 8 Y Tyrosine
11 1 19 V Valine
4 3 13 A Alanine 

3UFN_1|Chains A, B|HIV-1 protease|Homo sapiens (9606)
>1JZA_1|Chains A, B|NEUROTOXIN 2|Centruroides sculpturatus (218467)
>3ZQT_1|Chain A|ANDROGEN RECEPTOR|ESCHERICHIA COLI (469008)
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 \(w=f(c)\)
3UFN , Knot 52 99 0.80 36 80 95 
PQITLWKRPFVTVKVGGQLKEALLDTGADNTIFEDINLPGRWKPKMVGGIGGFLKVREYDQVPIEIAGHKVIGTVLVGPTPVNVIGRDTMTQIGATLNF
1JZA , Knot 37 66 0.78 32 53 63 
KEGYLVNKSTGCKYGCLKLGENEGCDKECKAKNQGGSYGYCYAFACWCEGLPESTPTYPLPNKSCS
3ZQT , Knot 122 256 0.88 40 189 248 
IEGYECQPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAEIISVQVPKILSGKVKPIYFHTQ

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 \(c\).

\(|P_{f(3UFN_1)}(2) \setminus P_{f(1JZA_1)}(2)|=71\), \(|P_{f(1JZA_1)}(2) \setminus P_{f(3UFN_1)}(2)|=44\). 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 1:101011001110101110100111001100011001011101010111111111010000011101110011101111101101110001001110101
Pair \(Z_2\) Length of longest common subsequence
3UFN_1,1JZA_1 115 2
3UFN_1,3ZQT_1 177 3
1JZA_1,3ZQT_1 190 3

Newick tree

 
[
	3ZQT_1:10.67,
	[
		3UFN_1:57.5,1JZA_1:57.5
	]:43.17
]

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 \((0.85)(0.8)(\frac{165 }{\log_{20} 165}-\frac{66}{\log_{20}66})=33.7\)
Status Protein1 Protein2 d d1/2
Query variables 3UFN_1 1JZA_1 44 36.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: