CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4LSV_1 1XSD_1 7FSR_1 Letter Amino acid
12 0 11 D Aspartic acid
30 6 12 T Threonine
7 0 1 W Tryptophan
26 0 9 E Glutamic acid
28 2 16 G Glycine
10 0 6 H Histidine
6 0 7 M Methionine
16 0 5 P Proline
23 0 15 S Serine
18 6 11 A Alanine
12 0 8 R Arginine
35 0 9 N Asparagine
25 0 25 I Isoleucine
22 0 15 K Lycine
20 0 12 V Valine
14 2 3 C Cysteine
11 0 9 Q Glutamine
23 0 13 L Leucine
12 0 8 F Phenylalanine
8 0 0 Y Tyrosine 

4LSV_1|Chain A[auth G]|envelope glycoprotein GP120|Human immunodeficiency virus 1 (11676)
>1XSD_1|Chain A[auth B]|5'-D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3'|
>7FSR_1|Chains A, B, C, D|Syntenin-1|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 \(w=f(c)\)
4LSV , Knot 155 358 0.84 40 209 337 
VWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNGGSGSGGNIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDGGQSNETNDTETFRPGGGDMRDNWRSELYKYKVVEIK
1XSD , Knot 8 16 0.46 8 8 12 
TACTACATATGTAGTA
7FSR , Knot 90 195 0.81 38 132 183 
SMAEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAFIFEHIIKRMAPSIMKSLMDHTIPEV

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 \(c\).

\(|P_{f(4LSV_1)}(2) \setminus P_{f(1XSD_1)}(2)|=202\), \(|P_{f(1XSD_1)}(2) \setminus P_{f(4LSV_1)}(2)|=1\). 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 1:1100100011010010100001001110010110010100111101000101100011001000110110001010101011011001010101011110001111111100000010101100010010000110111000111010110001110000100010011101000101100010011010110100100010000100010011001100110001010100110101000010001011000000110100001000001000010101000100110110011011011110101000001011111001100000000001011110100010001000011010
Pair \(Z_2\) Length of longest common subsequence
4LSV_1,1XSD_1 203 2
4LSV_1,7FSR_1 193 3
1XSD_1,7FSR_1 132 2

Newick tree

 
[
	4LSV_1:10.81,
	[
		7FSR_1:66,1XSD_1:66
	]:41.81
]

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 \((0.85)(0.8)(\frac{374 }{\log_{20} 374}-\frac{16}{\log_{20}16})=116.\)
Status Protein1 Protein2 d d1/2
Query variables 4LSV_1 1XSD_1 152 78.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]