CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5IZP_1 5LNU_1 6UAS_1 Letter Amino acid
0 17 12 D Aspartic acid
0 11 10 Q Glutamine
0 24 5 E Glutamic acid
0 0 8 W Tryptophan
4 5 0 C Cysteine
4 30 30 G Glycine
0 18 20 L Leucine
2 40 41 A Alanine
0 22 13 R Arginine
0 22 4 I Isoleucine
0 14 7 M Methionine
0 10 14 P Proline
0 10 24 S Serine
2 10 22 T Threonine
0 4 12 Y Tyrosine
0 11 5 N Asparagine
0 12 9 H Histidine
0 13 3 K Lycine
0 10 11 F Phenylalanine
0 33 13 V Valine 

5IZP_1|Chains A, B|DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')|synthetic construct (32630)
>5LNU_1|Chains A, B, C, D|Pyridoxal 5'-phosphate synthase subunit PDX1.3|Arabidopsis thaliana (3702)
>6UAS_1|Chain A|Glycoside Hydrolase|Amycolatopsis mediterranei (33910)
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 \(w=f(c)\)
5IZP , Knot 6 12 0.41 8 7 8 
CGCGAATTCGCG
5LNU , Knot 128 316 0.77 38 177 294 
MEGTGVVAVYGNGAITEAKKSPFSVKVGLAQMLRGGVIMDVVNAEQARIAEEAGACAVMALERVPADIRAQGGVARMSDPQMIKEIKQAVTIPVMAKARIGHFVEAQILEAIGIDYIDESEVLTLADEDHHINKHNFRIPFVCGCRNLGEALRRIREGAAMIRTKGEAGTGNIIEAVRHVRSVNGDIRVLRNMDDDEVFTFAKKLAAPYDLVMQTKQLGRLPVVQFAAGGVATPADAALMMQLGCDGVFVGSGIFKSGDPARRARAIVQAVTHYSDPEMLVEVSCGLGEAMVGINLNDEKVERFANRSEEHHHHHH
6UAS , Knot 109 263 0.77 38 149 235 
MGSSHHHHHHSSGLVPAGSHMAGTKKGVSAAAFSGVTAALGDVGARWFYTWAADPQGITAPAGTEFVPMIWGRDSVTADQLQRAKAAGSTLLAFNEPDLAGQANMSVETALDLWPQLQATGMRLGAPAVAYGGDTPGGWLDRFMSGAAARGYRVDFIPLHWYGGDFSAAATGQLQSYLQAVYNRYHRPIWLTAYALTDFSGSTPRYPSAAEQADFVSRSTAMLNGLSFVERYAWFSLSTSTTPTGLYTGTTPNSSGVAYRAAG

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 \(c\).

\(|P_{f(5IZP_1)}(2) \setminus P_{f(5LNU_1)}(2)|=2\), \(|P_{f(5LNU_1)}(2) \setminus P_{f(5IZP_1)}(2)|=172\). 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 1:010111000101
Pair \(Z_2\) Length of longest common subsequence
5IZP_1,5LNU_1 174 3
5IZP_1,6UAS_1 148 3
5LNU_1,6UAS_1 182 6

Newick tree

 
[
	5LNU_1:93.49,
	[
		5IZP_1:74,6UAS_1:74
	]:19.49
]

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 \((0.85)(0.8)(\frac{328 }{\log_{20} 328}-\frac{12}{\log_{20}12})=105.\)
Status Protein1 Protein2 d d1/2
Query variables 5IZP_1 5LNU_1 125 64.5
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: