CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6GVZ_1 2WRU_1 1PGN_1 Letter Amino acid
20 2 18 N Asparagine
7 0 12 H Histidine
2 0 13 M Methionine
6 0 8 W Tryptophan
7 2 13 Y Tyrosine
14 0 20 R Arginine
24 1 52 G Glycine
5 0 35 K Lycine
25 1 17 T Threonine
15 2 17 Q Glutamine
32 0 15 P Proline
18 1 24 V Valine
32 2 46 L Leucine
17 0 31 D Aspartic acid
3 4 9 C Cysteine
11 2 23 E Glutamic acid
14 2 35 I Isoleucine
17 0 23 F Phenylalanine
22 2 27 S Serine
14 0 44 A Alanine 

6GVZ_1|Chain A|Capsid protein VP1|Norovirus Hu/GII.1/7EK/Hawaii/1971/USA (1208060)
>2WRU_1|Chain A|INSULIN A CHAIN|HOMO SAPIENS (9606)
>1PGN_1|Chain A|6-PHOSPHOGLUCONATE DEHYDROGENASE|Ovis aries (9940)
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 \(w=f(c)\)
6GVZ , Knot 133 305 0.83 40 185 296 
GPGSKPFTLPILTIGELSNSRFPVPIDELYTSPNEGVIVQPQNGRSTLDGELLGTTQLVPSNICALRGRINAQVPDDHHQWNLQVTNTNGTPFDPTEDVPAPLGTPDFLANIYGVTSQRNPNNTCRAHDGVLATWSPKFTPKLGSVILGTWEESDLDLNQPTRFTPVGLFNTDHFDQWALPSYSGRLTLNMNLAPSVSPLFPGEQLLFFRSHIPLKGGTSDGAIDCLLPQEWIQHFYQESAPSPTDVALIRYTNPDTGRVLFEAKLHRQGFITVANSGSRPIVVPPNGYFRFDSWVNQFYSLAPM
2WRU , Knot 15 21 0.72 22 20 19 
GIVEQCCTSICSLYQLENYCN
1PGN , Knot 198 482 0.84 40 251 457 
AQADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVLGAHSLEEMVSKLKKPRRIILLVKAGQAVDNFIEKLVPLLDIGDIIIDGGNSEYRDTMRRCRDLKDKGILFVGSGVSGGEDGARYGPSLMPGGNKEAWPHIKAIFQGIAAKVGTGEPCCDWVGDDGAGHFVKMVHNGIEYGDMQLICEAYHLMKDVLGLGHKEMAKAFEEWNKTELDSFLIEITASILKFQDADGKHLLPKIRDSAGQKGTGKWTAISALEYGVPVTLIGEAVFARCLSSLKDERIQASKKLKGPQNIPFEGDKKSFLEDIRKALYASKIISYAQGFMLLRQAATEFGWTLNYGGIALMWRGGCIIRSVFLGKIKDAFDRNPGLQNLLLDDFFKSAVENCQDSWRRAISTGVQAGIPMPCFTTALSFYDGYRHAMLPANLIQAQRDYFGAHTYELLAKPGQFIHTNWTGHGGSVSSSSYNA

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 \(c\).

\(|P_{f(6GVZ_1)}(2) \setminus P_{f(2WRU_1)}(2)|=177\), \(|P_{f(2WRU_1)}(2) \setminus P_{f(6GVZ_1)}(2)|=12\). 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 1:11100110111101101000011111001000100111101001000101011100011100101101010101100000101010000101101000111111010111010110000010000010011110101010101101111010000101001001011111000010011110001010101011101011111001111000111011000111001110011001000011010011110000100101110101000111011001001111110101010011001001111
Pair \(Z_2\) Length of longest common subsequence
6GVZ_1,2WRU_1 189 2
6GVZ_1,1PGN_1 184 5
2WRU_1,1PGN_1 249 2

Newick tree

 
[
	2WRU_1:11.04,
	[
		6GVZ_1:92,1PGN_1:92
	]:24.04
]

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 \((0.85)(0.8)(\frac{326 }{\log_{20} 326}-\frac{21}{\log_{20}21})=100.\)
Status Protein1 Protein2 d d1/2
Query variables 6GVZ_1 2WRU_1 127 68.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]