CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5XJK_1 1XYE_1 3PBU_1 Letter Amino acid
0 1 3 C Cysteine
4 1 3 Q Glutamine
2 3 10 M Methionine
3 3 20 R Arginine
2 0 21 I Isoleucine
6 18 17 L Leucine
7 11 7 K Lycine
7 7 9 F Phenylalanine
5 7 10 P Proline
3 11 11 S Serine
0 1 0 W Tryptophan
3 4 16 E Glutamic acid
3 4 7 N Asparagine
2 8 18 D Aspartic acid
4 7 21 G Glycine
5 9 7 T Threonine
3 2 4 Y Tyrosine
3 12 17 V Valine
3 22 25 A Alanine
0 10 2 H Histidine 

5XJK_1|Chain A|Spike protein S2|Human SARS coronavirus (694009)
>1XYE_1|Chains A, C|Hemoglobin alpha chain|Homo sapiens (9606)
>3PBU_1|Chains A, B|Orotidine 5'-monophosphate decarboxylase|Methanobacterium thermoautotrophicum (187420)
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 \(w=f(c)\)
5XJK , Knot 36 65 0.77 34 58 63 
PRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPSPLKPTKRSFIEDLLFNKVTLADAGFMKQYGE
1XYE , Knot 68 141 0.79 38 100 137 
MLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTAFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
3PBU , Knot 99 228 0.78 38 145 217 
MRSRRVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAISVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLNP

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 \(c\).

\(|P_{f(5XJK_1)}(2) \setminus P_{f(1XYE_1)}(2)|=35\), \(|P_{f(1XYE_1)}(2) \setminus P_{f(5XJK_1)}(2)|=77\). 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 1:10000011101001000101001111010011101101000011001110010110111100010
Pair \(Z_2\) Length of longest common subsequence
5XJK_1,1XYE_1 112 4
5XJK_1,3PBU_1 145 4
1XYE_1,3PBU_1 149 4

Newick tree

 
[
	3PBU_1:78.47,
	[
		5XJK_1:56,1XYE_1:56
	]:22.47
]

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 \((0.85)(0.8)(\frac{206 }{\log_{20} 206}-\frac{65}{\log_{20}65})=47.0\)
Status Protein1 Protein2 d d1/2
Query variables 5XJK_1 1XYE_1 55 40.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: