CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7QIW_1 2MFR_1 8FLG_1 Letter Amino acid
8 3 24 S Serine
10 7 13 I Isoleucine
20 2 21 K Lycine
8 5 12 F Phenylalanine
15 4 11 P Proline
9 1 9 N Asparagine
7 1 12 Q Glutamine
1 0 6 W Tryptophan
11 6 29 L Leucine
12 2 11 T Threonine
24 5 19 V Valine
27 1 13 A Alanine
7 3 14 D Aspartic acid
5 0 6 C Cysteine
34 3 19 G Glycine
7 4 16 Y Tyrosine
27 2 14 R Arginine
8 1 25 E Glutamic acid
14 6 6 H Histidine
6 1 13 M Methionine 

7QIW_1|Chain A[auth D]|60S ribosomal protein L8|Solanum lycopersicum (4081)
>2MFR_1|Chain A|Insulin receptor|Homo sapiens (9606)
>8FLG_1|Chain A|Tyrosine-protein kinase BTK|Homo sapiens (9606)
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 \(w=f(c)\)
7QIW , Knot 119 260 0.84 40 172 251 
MGRVIRAQRKGAGSVFKSHTHHRKGPARFRTLDFGERNGYLKGVITEVIHDPGRGAPLARVTFRHPFRYKHQKELFVAAEGMYTGQFVYCGKKATLMVGNVLPLRSIPEGAVVCNVEHKVGDRGVFARCSGDYAIVISHNPDNGTTRVKLPSGAKKIVPSGCRAMIGQVAGGGRTEKPMLKAGNAYHKYRVKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKVGLIAARRTGRLRGQARATAAKADKA
2MFR , Knot 32 57 0.75 36 45 51 
MTYFYVTDYLDVPSNIAKIIIGPLIFVFLFSVVIGSIYLFLRKRQPDGPLEHHHHHH
8FLG , Knot 132 293 0.85 40 200 283 
GPLGSRLKYPVSQQNKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES

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 \(c\).

\(|P_{f(7QIW_1)}(2) \setminus P_{f(2MFR_1)}(2)|=145\), \(|P_{f(2MFR_1)}(2) \setminus P_{f(7QIW_1)}(2)|=18\). 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 1:11011010001110110000000011101001011000101011100110011011111010100110000000111110110010110010010111101111001101111001000110011110001001111000100100010110110011101001111011111000011101101000001000011010111101100101110000110100100011110011111100010101010101101001
Pair \(Z_2\) Length of longest common subsequence
7QIW_1,2MFR_1 163 3
7QIW_1,8FLG_1 198 4
2MFR_1,8FLG_1 199 3

Newick tree

 
[
	8FLG_1:10.49,
	[
		7QIW_1:81.5,2MFR_1:81.5
	]:22.99
]

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 \((0.85)(0.8)(\frac{317 }{\log_{20} 317}-\frac{57}{\log_{20}57})=83.4\)
Status Protein1 Protein2 d d1/2
Query variables 7QIW_1 2MFR_1 108 64
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]