CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2KZM_1 3CRG_1 3QKJ_1 Letter Amino acid
0 7 9 D Aspartic acid
2 13 18 G Glycine
0 11 3 H Histidine
0 8 7 P Proline
0 1 7 W Tryptophan
0 8 3 Y Tyrosine
1 6 12 A Alanine
0 6 5 R Arginine
0 7 8 E Glutamic acid
0 5 8 V Valine
2 8 5 T Threonine
0 6 6 Q Glutamine
0 1 5 M Methionine
0 5 9 F Phenylalanine
0 17 11 L Leucine
0 10 14 K Lycine
0 10 14 S Serine
0 9 4 N Asparagine
3 3 0 C Cysteine
0 5 3 I Isoleucine 

2KZM_1|Chain A[auth B]|DNA (5'-D(*GP*CP*TP*TP*A*CP*GP*C)-3')|
>3CRG_1|Chains A, B|Heparin-binding growth factor 1|Homo sapiens (9606)
>3QKJ_1|Chains A, B, C, D|DNA cytosine-5 methyltransferase 3 beta isoform 6 variant|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 \(w=f(c)\)
2KZM , Knot 6 8 0.52 8 6 6 
GCTTACGC
3CRG , Knot 72 146 0.82 40 113 138 
HHHHHHFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTDGLLYGSQTPNANCLFLERLEENHYNTYISKAHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPVSSD
3QKJ , Knot 72 151 0.79 38 110 144 
GEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP

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 \(c\).

\(|P_{f(2KZM_1)}(2) \setminus P_{f(3CRG_1)}(2)|=6\), \(|P_{f(3CRG_1)}(2) \setminus P_{f(2KZM_1)}(2)|=113\). 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 1:10001010
Pair \(Z_2\) Length of longest common subsequence
2KZM_1,3CRG_1 119 1
2KZM_1,3QKJ_1 116 1
3CRG_1,3QKJ_1 155 4

Newick tree

 
[
	3CRG_1:72.40,
	[
		2KZM_1:58,3QKJ_1:58
	]:14.40
]

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 \((0.85)(0.8)(\frac{154 }{\log_{20} 154}-\frac{8}{\log_{20}8})=54.4\)
Status Protein1 Protein2 d d1/2
Query variables 2KZM_1 3CRG_1 69 36
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: