CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8IVK_1 2VNO_1 4WKP_1 Letter Amino acid
12 14 11 D Aspartic acid
7 5 8 Q Glutamine
10 12 20 E Glutamic acid
5 14 20 S Serine
5 3 3 R Arginine
4 12 7 N Asparagine
8 13 17 I Isoleucine
3 16 19 K Lycine
1 9 3 Y Tyrosine
3 13 22 V Valine
5 12 20 A Alanine
2 0 3 C Cysteine
3 2 14 H Histidine
10 11 23 L Leucine
1 1 6 M Methionine
5 7 17 F Phenylalanine
1 7 5 P Proline
9 14 19 G Glycine
7 13 8 T Threonine
5 2 0 W Tryptophan 

8IVK_1|Chain A|Iron-sulfur cluster assembly protein CyaY|Escherichia coli (562)
>2VNO_1|Chains A, B|CPE0329|CLOSTRIDIUM PERFRINGENS (1502)
>4WKP_1|Chains A, B, C, D|Aminodeoxyfutalosine nucleosidase|Helicobacter pylori (85963)
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 \(w=f(c)\)
8IVK , Knot 55 106 0.80 40 87 102 
MNDSEFHRLADQLWLTIEERLDDWDGDSDIDCEINGGVLTITFENGSKIIINRQEPLHQVWLATKQGGYHFDLKGDEWICDRSGETFWDLLEQAATQQAGETVSFR
2VNO , Knot 87 180 0.83 38 129 174 
EVYALEESRDVYLSDLDWLNATHGDDTKSKIVQKNHPFTPGNNNQSTKISLKMEDGSISEFEKGLGTIAGSPSTITYDISGAGVTKFFSYLGIDRSANPINEQYAKVDKIEVVVDGKVIYSTINQFPNGLTYETPAIKVDLNIPENAKRLQLKSYAGEKTWGDEVVYADAKFTAKGDFVN
4WKP , Knot 104 245 0.77 38 153 230 
MGHHHHHHENLYFQGVQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL

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 \(c\).

\(|P_{f(8IVK_1)}(2) \setminus P_{f(2VNO_1)}(2)|=46\), \(|P_{f(2VNO_1)}(2) \setminus P_{f(8IVK_1)}(2)|=88\). 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 1:1000010011001110100010010100010001011110101001001110000110011110001100101010011000010011011001100011001010
Pair \(Z_2\) Length of longest common subsequence
8IVK_1,2VNO_1 134 3
8IVK_1,4WKP_1 150 3
2VNO_1,4WKP_1 142 3

Newick tree

 
[
	4WKP_1:74.92,
	[
		8IVK_1:67,2VNO_1:67
	]:7.92
]

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 \((0.85)(0.8)(\frac{286 }{\log_{20} 286}-\frac{106}{\log_{20}106})=56.7\)
Status Protein1 Protein2 d d1/2
Query variables 8IVK_1 2VNO_1 70 55
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]