CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3RIV_1 1UEB_1 6CLG_1 Letter Amino acid
10 7 0 Y Tyrosine
22 8 0 D Aspartic acid
18 21 1 G Glycine
7 1 0 H Histidine
20 12 0 K Lycine
16 11 0 P Proline
17 5 1 S Serine
10 2 3 N Asparagine
6 6 1 Q Glutamine
18 21 0 E Glutamic acid
27 12 0 L Leucine
7 6 0 M Methionine
7 1 0 C Cysteine
13 7 1 F Phenylalanine
12 16 0 T Threonine
21 9 0 A Alanine
14 9 0 R Arginine
10 4 0 I Isoleucine
5 1 0 W Tryptophan
11 25 0 V Valine 

3RIV_1|Chains A, B|Ascorbate peroxidase|Leishmania major (347515)
>1UEB_1|Chains A, B|elongation factor P|Thermus thermophilus (274)
>6CLG_1|Chain A|GSNQNNF|synthetic construct (32630)
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 \(w=f(c)\)
3RIV , Knot 122 271 0.84 40 184 259 
TSEEPPFDIRALRADIEDMISEKLELGPSLIRLAWHEAASYDCFKKDGSPNSASMRFKPECLYAGNKGLDIPRKALETLKKKYPQISYADLWVLAAYVAIEYMGGPTIPFCWGRVDAKDGSVCGPDGRLPDGSKTQSHVREVFRRLGFNDQETVALIGAHTCGECHIEFSGYHGPWTHDKNGFDNSFFTQLLDEDWVLNPKVEQMQLMDRATTKLMMLPSDVCLLLDPSYRKYVELYAKDNDRFNKDFANAFKKLTELGTRNLHKAPASES
1UEB , Knot 86 184 0.81 40 122 174 
MISVTDLRPGTKVKMDGGLWECVEYQHQKLGRGGAKVVAKFKNLETGATVERTFNSGEKLEDIYVETRELQYLYPEGEEMVFMDLETYEQFAVPRSRVVGAEFFKEGMTALGDMYEGQPIKVTPPTVVELKVVDTPPGVRGDTVSGGSKPATLETGAVVQVPLFVEPGEVIKVDTRTGEYVGRA
6CLG , Knot 6 7 0.55 10 6 5 
GSNQNNF

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 \(c\).

\(|P_{f(3RIV_1)}(2) \setminus P_{f(1UEB_1)}(2)|=118\), \(|P_{f(1UEB_1)}(2) \setminus P_{f(3RIV_1)}(2)|=56\). 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 1:0000111010110101001100010111011011100110000100010100101010100101100110110011001000010100101111110111001111011101101010010101101011010000001001100111000001111110001000101010011100000110001100110001110101001011001000111110010111010000010101000001000110110010011000100111000
Pair \(Z_2\) Length of longest common subsequence
3RIV_1,1UEB_1 174 4
3RIV_1,6CLG_1 188 2
1UEB_1,6CLG_1 126 2

Newick tree

 
[
	3RIV_1:98.04,
	[
		1UEB_1:63,6CLG_1:63
	]:35.04
]

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 \((0.85)(0.8)(\frac{455 }{\log_{20} 455}-\frac{184}{\log_{20}184})=79.5\)
Status Protein1 Protein2 d d1/2
Query variables 3RIV_1 1UEB_1 107 86.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]