CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6VLR_1 3FUR_1 2EHR_1 Letter Amino acid
22 8 4 R Arginine
20 1 0 C Cysteine
20 16 4 Q Glutamine
31 16 14 S Serine
46 8 7 N Asparagine
17 18 3 D Aspartic acid
33 21 11 I Isoleucine
28 38 8 L Leucine
43 13 4 T Threonine
10 0 1 W Tryptophan
34 14 12 V Valine
20 16 6 A Alanine
23 19 8 E Glutamic acid
31 11 13 G Glycine
9 9 0 M Methionine
16 15 4 F Phenylalanine
12 8 0 Y Tyrosine
9 6 2 H Histidine
29 24 8 K Lycine
22 11 8 P Proline 

6VLR_1|Chains A, C[auth G], E[auth H]|Envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676)
>3FUR_1|Chain A|Peroxisome proliferator-activated receptor gamma|Homo sapiens (9606)
>2EHR_1|Chain A|InaD-like protein|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 \(w=f(c)\)
6VLR , Knot 195 475 0.84 40 236 443 
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHCCVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQWFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVG
3FUR , Knot 120 272 0.82 38 172 260 
PESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
2EHR , Knot 58 117 0.78 34 87 113 
GSSGSSGPNFSHWGPPRIVEIFREPNVSLGISIVGGQTVIKRLKNGEELKGIFIKQVLEDSPAGKTNALKTGDKILEVSGVDLQNASHSEAVEAIKNAGNPVVFIVQSLSSTPRVIP

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 \(c\).

\(|P_{f(6VLR_1)}(2) \setminus P_{f(3FUR_1)}(2)|=120\), \(|P_{f(3FUR_1)}(2) \setminus P_{f(6VLR_1)}(2)|=56\). 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 1:1001110100111110010001101001010000000111000011001010010100100010110001100100011011000101010101101010000100010001010100001010001000000100110010110100001000000000001100000110010101010111100011111111000000101011010100100001101110001110101100011100001000100111010011010000100000001011110110101011101001000100101000110110010001100011011000110101000010011011000001110001100001010000100001011001001101100110110111101110010010111100011000000001011110100010001000011010111111000000111
Pair \(Z_2\) Length of longest common subsequence
6VLR_1,3FUR_1 176 3
6VLR_1,2EHR_1 197 3
3FUR_1,2EHR_1 159 3

Newick tree

 
[
	6VLR_1:97.59,
	[
		3FUR_1:79.5,2EHR_1:79.5
	]:18.09
]

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 \((0.85)(0.8)(\frac{747 }{\log_{20} 747}-\frac{272}{\log_{20}272})=131.\)
Status Protein1 Protein2 d d1/2
Query variables 6VLR_1 3FUR_1 164 130
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]