CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2GVI_1 4AEY_1 2MIX_1 Letter Amino acid
17 6 1 K Lycine
6 5 0 M Methionine
2 0 1 W Tryptophan
14 4 1 Y Tyrosine
7 10 1 V Valine
11 12 1 R Arginine
6 0 6 C Cysteine
9 14 1 I Isoleucine
11 5 0 F Phenylalanine
15 12 0 A Alanine
19 15 0 E Glutamic acid
21 6 2 G Glycine
11 9 0 P Proline
10 3 3 S Serine
6 8 1 T Threonine
2 3 1 Q Glutamine
4 10 0 H Histidine
16 18 0 L Leucine
6 8 1 N Asparagine
11 8 1 D Aspartic acid 

2GVI_1|Chain A|conserved hypothetical protein|Thermoplasma acidophilum (2303)
>4AEY_1|Chain A|D-ERYTHRO-7,8-DIHYDRONEOPTERIN TRIPHOSPHATE EPIMERASE|PSEUDOMONAS AERUGINOSA (287)
>2MIX_1|Chain A|venom peptide toxin|Terebridae (57610)
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 \(w=f(c)\)
2GVI , Knot 98 204 0.85 40 146 200 
GMEKLNFGIPEWAFEFHGHKCPYMPMGYRAGSYALKIAGLEKEKDHRTYLLSEMSPEDMNGCFNDGAQAATGCTYGKGLFSLLGYGKLALILYRPGRKAIRVHVRNSFMDELSTRASDFFRYRKQGYEPSEIPAGAIDPVLEWISSLEDEEIFEYREIDGFTFEPVKKNGAKVRCDVCGEYTYEADAKLLNGKPVCKPDYYGKK
4AEY , Knot 74 156 0.79 36 115 147 
MHHHHHHGKPIPNPLLGLDSTENLYFQGIDPFTMPRLEPGMARIRVKDLRLRTFIGIKEEEILNKQDVLINLTILYPAADAVEVNDIEHALNYRTITKAIIRHVEENRFALLERMTQEILDLVMENPAVRYAEVEVDKPHALRFAESVSITLAGHR
2MIX , Knot 16 21 0.77 26 19 19 
TRICCGCYWNGSKDVCSQSCC

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 \(c\).

\(|P_{f(2GVI_1)}(2) \setminus P_{f(4AEY_1)}(2)|=94\), \(|P_{f(4AEY_1)}(2) \setminus P_{f(2GVI_1)}(2)|=63\). 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 1:110010111101110101000101111001100110111100000000011001010010101001101101000101110111010111110011001101010001100100010011000001001001111110111011001000011000010110101100011010001010000010101101011001000100
Pair \(Z_2\) Length of longest common subsequence
2GVI_1,4AEY_1 157 3
2GVI_1,2MIX_1 149 3
4AEY_1,2MIX_1 128 2

Newick tree

 
[
	2GVI_1:80.26,
	[
		2MIX_1:64,4AEY_1:64
	]:16.26
]

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 \((0.85)(0.8)(\frac{360 }{\log_{20} 360}-\frac{156}{\log_{20}156})=61.6\)
Status Protein1 Protein2 d d1/2
Query variables 2GVI_1 4AEY_1 81 70
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]