CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2LVE_1 4JAD_1 3CPB_1 Letter Amino acid
3 17 8 N Asparagine
5 28 18 D Aspartic acid
9 8 8 Q Glutamine
8 29 15 T Threonine
9 16 11 Y Tyrosine
8 29 20 G Glycine
0 14 16 H Histidine
6 24 21 K Lycine
3 22 15 F Phenylalanine
18 23 14 S Serine
2 3 5 W Tryptophan
6 36 22 A Alanine
4 24 21 R Arginine
4 27 22 E Glutamic acid
9 35 34 L Leucine
6 19 16 P Proline
6 19 17 V Valine
2 7 8 C Cysteine
5 28 15 I Isoleucine
1 18 8 M Methionine 

2LVE_1|Chain A|RLEN|Homo sapiens (9606)
>4JAD_1|Chains A, B|Citrate synthase|Escherichia coli (83333)
>3CPB_1|Chains A, B|Vascular endothelial growth factor receptor 2|Homo sapiens (9606)
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 \(w=f(c)\)
2LVE , Knot 59 114 0.81 38 92 110 
DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNSKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPYSFGQGTKLEIKR
4JAD , Knot 181 426 0.85 40 239 410 
ADTKAKLTLDGDTAVELDVLKGTLGQDVIDIRTLGSKGVFTFDPGFTSTTSCESKITFIDGDEGILLHRGFPIDQLATDSNYLEVCYILLNGEKPTQEQYDEFKTTVTRHTMIHEQITRLFHAFRRDSHPMAVMCGITGALAAFYHDSLDVNNPRHREIAAFRLLSKMPTMAAMCYKYSIGQPFVYPRNDLSYAGNFLNMMFSTPCEPYEVNPILERAMDRILILHADHEQNASTSTVRTAGSSGANPFACIAAGIASLWGPAHGGANEAALKMLEEIGKKENIPEFVRRAKDKNDSFRLMGFGHRVYKNYDPRATVMRETCHEVLKELGTKDDLLEVAMELENIALNDPYFIEKKLYPNVDFYSGIILKAMGIPSSMFTVIFAMARTVGWIAHWSEMHSDGMKIARPRQLYTGYEKRDFKSDIKR
3CPB , Knot 139 314 0.84 40 202 293 
EHAERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITEFCKFGNLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQQDRHHHHHH

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 \(c\).

\(|P_{f(2LVE_1)}(2) \setminus P_{f(4JAD_1)}(2)|=34\), \(|P_{f(4JAD_1)}(2) \setminus P_{f(2LVE_1)}(2)|=181\). 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 1:011100010011101100101000000011000000001110000110110111011000001110010101010010101001010011100000000010011010010100
Pair \(Z_2\) Length of longest common subsequence
2LVE_1,4JAD_1 215 3
2LVE_1,3CPB_1 182 3
4JAD_1,3CPB_1 161 3

Newick tree

 
[
	2LVE_1:10.18,
	[
		3CPB_1:80.5,4JAD_1:80.5
	]:24.68
]

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 \((0.85)(0.8)(\frac{540 }{\log_{20} 540}-\frac{114}{\log_{20}114})=125.\)
Status Protein1 Protein2 d d1/2
Query variables 2LVE_1 4JAD_1 163 102.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]