CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8XQB_1 1PRN_1 1GYB_1 Letter Amino acid
2 4 0 W Tryptophan
7 10 5 E Glutamic acid
6 14 14 L Leucine
0 4 3 K Lycine
2 19 7 Y Tyrosine
10 26 7 V Valine
4 16 9 N Asparagine
11 29 10 D Aspartic acid
3 9 12 Q Glutamine
14 35 5 G Glycine
1 0 2 H Histidine
5 16 10 F Phenylalanine
5 1 5 P Proline
9 25 9 S Serine
9 35 5 A Alanine
7 22 8 T Threonine
1 0 0 C Cysteine
6 13 6 I Isoleucine
2 3 3 M Methionine
13 8 5 R Arginine 

8XQB_1|Chains A[auth f], EA[auth f1], G[auth f2], M[auth f3], S[auth f4], Y[auth f5]|Head-tail connector protein FII|Escherichia phage Lambda (2681611)
>1PRN_1|Chain A|PORIN|Rhodobacter blasticus (1075)
>1GYB_1|Chains A, B, C, D|NUCLEAR TRANSPORT FACTOR 2|SACCHAROMYCES CEREVISIAE (4932)
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 \(w=f(c)\)
8XQB , Knot 57 117 0.77 38 90 113 
MADFDNLFDAAIARADETIRGYMGTSATITSGEQSGAVIRGVFDDPENISYAGQGVRVEGSSPSLFVRTDEVRQLRRGDTLTIGEENFWVDRVSPDDGGSCHLWLGRGVPPAVNRRR
1PRN , Knot 122 289 0.79 36 151 273 
EISLNGYGRFGLQYVEDRGVGLEDTIISSRLRINIVGTTETDQGVTFGAKLRMQWDDGDAFAGTAGNAAQFWTSYNGVTVSVGNVDTAFDSVALTYDSEMGYEASSFGDAQSSFFAYNSKYDASGALDNYNGIAVTYSISGVNLYLSYVDPDQTVDSSLVTEEFGIAADWSNDMISLAAAYTTDAGGIVDNDIAFVGAAYKFNDAGTVGLNWYDNGLSTAGDQVTLYGNYAFGATTVRAYVSDIDRAGADTAYGIGADYQFAEGVKVSGSVQSGFANETVADVGVRFDF
1GYB , Knot 64 125 0.82 36 106 122 
MSLDFNTLAQNFTQFYYNQFDTDRSQLGNLYRNESMLTFETSQLQGAKDIVEKLVSLPFQKVQHRITTLDAQPASPYGDVLVMITGDLLIDEEQNPQRFSQVFHLIPDGNSYYVFNDIFRLNYSA

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 \(c\).

\(|P_{f(8XQB_1)}(2) \setminus P_{f(1PRN_1)}(2)|=36\), \(|P_{f(1PRN_1)}(2) \setminus P_{f(8XQB_1)}(2)|=97\). 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 1:110100110111101000101011001010010001111011100100100110110101001011100001001001001011000111001010011000111101111110000
Pair \(Z_2\) Length of longest common subsequence
8XQB_1,1PRN_1 133 3
8XQB_1,1GYB_1 132 2
1PRN_1,1GYB_1 147 3

Newick tree

 
[
	1PRN_1:71.39,
	[
		8XQB_1:66,1GYB_1:66
	]:5.39
]

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 \((0.85)(0.8)(\frac{406 }{\log_{20} 406}-\frac{117}{\log_{20}117})=87.6\)
Status Protein1 Protein2 d d1/2
Query variables 8XQB_1 1PRN_1 104 73
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]