CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4AVJ_1 1RWD_1 1RIQ_1 Letter Amino acid
2 4 4 C Cysteine
4 5 37 K Lycine
14 2 21 S Serine
14 1 15 T Threonine
20 3 33 V Valine
12 3 23 A Alanine
1 0 16 H Histidine
2 1 5 W Tryptophan
2 6 54 E Glutamic acid
5 0 10 Q Glutamine
13 5 38 G Glycine
10 1 40 L Leucine
0 0 9 M Methionine
10 5 19 P Proline
10 3 20 Y Tyrosine
14 1 15 N Asparagine
7 7 21 D Aspartic acid
8 4 29 I Isoleucine
6 2 28 F Phenylalanine
4 0 28 R Arginine 

4AVJ_1|Chains A, B|FIMH|ESCHERICHIA COLI (364106)
>1RWD_1|Chain A|Rubredoxin|Pyrococcus furiosus (2261)
>1RIQ_1|Chain A|Alanyl-tRNA synthetase|Aquifex aeolicus (63363)
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 \(w=f(c)\)
4AVJ , Knot 73 158 0.78 38 115 153 
FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT
1RWD , Knot 30 53 0.75 32 46 50 
AKYVCKICGYIYDEDAGDPDNGVSPGTKFEEIPDDWVCPICGAPKSEFEKLED
1RIQ , Knot 193 465 0.85 40 236 435 
MSLSAHEIRELFLSFFEKKGHTRVKSAPLVPENDPTLLFVNAGMVPFKNVFLGLEKRPYKRATSCQKCLRVSGKHNDLEQVGYTSRHHTFFEMLGNFSFGDYFKKEAIEYAWEFVTEVLKLPKEKLYVSVYKDDEEAYRIWNEHIGIPSERIWRLGEEDNFWQMGDVGPCGPSSEIYVDRGEEYEGDERYLEIWNLVFMQYNRDENGVLTPLPHPNIDTGMGLERIASVLQGKNSNFEIDIIFPLIQFGEEVSGKKYGEKFETDVALRVIADHLRAITFAISDGVIPSNEGRGYVIRRILRRAMRFGYKLGIENPFLYKGVDLVVDIMKEPYPELELSREFVKGIVKGEEKRFIKTLKAGMEYIQEVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEIAREKGLGIDLEGFQCELEEQRERARKHFKVEAKKVKPVYSHLKELGKTSAFVGAAALEHHHHHH

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 \(c\).

\(|P_{f(4AVJ_1)}(2) \setminus P_{f(1RWD_1)}(2)|=101\), \(|P_{f(1RWD_1)}(2) \setminus P_{f(4AVJ_1)}(2)|=32\). 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 1:11000101011111110101010111110110011101000110000010010001010010101111001010100010001110000010110000000111111010110011111101101111111000000000010111010100011110
Pair \(Z_2\) Length of longest common subsequence
4AVJ_1,1RWD_1 133 2
4AVJ_1,1RIQ_1 185 4
1RWD_1,1RIQ_1 218 3

Newick tree

 
[
	1RIQ_1:11.23,
	[
		4AVJ_1:66.5,1RWD_1:66.5
	]:43.73
]

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 \((0.85)(0.8)(\frac{211 }{\log_{20} 211}-\frac{53}{\log_{20}53})=53.1\)
Status Protein1 Protein2 d d1/2
Query variables 4AVJ_1 1RWD_1 64 43
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]