CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5VYP_1 4ZKJ_1 5WAY_1 Letter Amino acid
4 9 10 P Proline
4 17 18 T Threonine
1 19 29 N Asparagine
2 16 24 D Aspartic acid
0 10 21 Q Glutamine
1 9 26 H Histidine
2 31 57 L Leucine
2 19 43 F Phenylalanine
5 12 16 R Arginine
4 18 40 I Isoleucine
7 19 31 K Lycine
2 21 49 S Serine
8 4 7 C Cysteine
2 16 44 E Glutamic acid
2 15 8 G Glycine
0 3 4 W Tryptophan
0 13 23 Y Tyrosine
0 18 26 V Valine
2 12 12 A Alanine
0 10 13 M Methionine 

5VYP_1|Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X|Defensin NsD7|Nicotiana suaveolens (200320)
>4ZKJ_1|Chains A, B|CRISPR-associated protein Cas1|Streptococcus pyogenes M1 476 (1207470)
>5WAY_1|Chains A, B|Transcriptional activator|Streptococcus pneumoniae (1313)
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 \(w=f(c)\)
5VYP , Knot 30 48 0.80 30 42 45 
AKDCKRESNTFPGICITKPPCRKACIREKFTDGHCSKILRRCLCTKPC
4ZKJ , Knot 131 291 0.85 40 198 281 
GHMAGWRTVVVNTHSKLSYKNNHLIFKDAYKTELIHLSEIDILLLETTDIVLSTMLVKRLVDENVLVIFCDDKRLPTAMLMPFYGRHDSSLQLGKQMSWSETVKSQVWTTIIAQKILNQSCYLGACSYFEKSQSIMDLYHGLENFDPSNREGHAARIYFNTLFGNDFSRDLEHPINAGLDYGYTLLLSMFAREVVVSGCMTQFGLKHANQFNQFNFASDIMEPFRPLVDKIVYENRNQPFPKIKRELFTLFSDTFSYNGKEMYLTNIISDYTKKVVKALNNEGKGVPEFRI
5WAY , Knot 193 501 0.79 40 230 455 
MRDLLSKKSHRQLELLELLFEHKRWFHRSELAELLNCTERAVKDDLSHVKSAFPDLIFHSSTNGIRIINTDDSDIEMVYHHFFKHSTHFSILEFIFFNEGCQAESICKEFYISSSSLYRIISQINKVIKRQFQFEVSLTPVQIIGNERDIRYFFAQYFSEKYYFLEWPFENFSSEPLSQLLELVYKETSFPMNLSTHRMLKLLLVTNLYRIKFGHFMEVDKDSFNDQSLDFLMQAEGIEGVAQSFESEYNISLDEEVVCQLFVSYFQKMFFIDESLFMKCVKKDSYVEKSYHLLSDFIDQISVKYQIEIENKDNLIWHLHNTAHLYRQELFTEFILFDQKGNTIRNFQNIFPKFVSDVKKELSHYLETLEVCSSSMMVNHLSYTFITHTKHLVINLLQNQPKLKVLVMSNFDQYHAKFVAETLSYYCSNNFELEVWTELELSKESLEDSPYDIIISNFIIPPIENKRLIYSNNINTVSLIYLLNAMMFIRLDEAGHHHHHH

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 \(c\).

\(|P_{f(5VYP_1)}(2) \setminus P_{f(4ZKJ_1)}(2)|=24\), \(|P_{f(4ZKJ_1)}(2) \setminus P_{f(5VYP_1)}(2)|=180\). 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 1:100000000011110100110001010001001000011000100010
Pair \(Z_2\) Length of longest common subsequence
5VYP_1,4ZKJ_1 204 3
5VYP_1,5WAY_1 224 2
4ZKJ_1,5WAY_1 162 4

Newick tree

 
[
	5VYP_1:11.50,
	[
		4ZKJ_1:81,5WAY_1:81
	]:33.50
]

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 \((0.85)(0.8)(\frac{339 }{\log_{20} 339}-\frac{48}{\log_{20}48})=93.2\)
Status Protein1 Protein2 d d1/2
Query variables 5VYP_1 4ZKJ_1 123 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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: