CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6VBI_1 2IAK_1 9IQR_1 Letter Amino acid
9 2 8 C Cysteine
21 17 1 Q Glutamine
12 9 2 H Histidine
43 30 2 L Leucine
4 6 1 W Tryptophan
16 12 3 R Arginine
17 8 2 D Aspartic acid
10 11 2 V Valine
9 4 4 P Proline
16 18 1 S Serine
9 6 0 M Methionine
16 10 9 T Threonine
17 12 5 N Asparagine
24 31 4 E Glutamic acid
23 10 6 I Isoleucine
21 15 4 K Lycine
16 3 2 F Phenylalanine
7 5 3 Y Tyrosine
27 14 3 A Alanine
8 1 3 G Glycine 

6VBI_1|Chains A, B|cGMP-specific 3',5'-cyclic phosphodiesterase|Homo sapiens (9606)
>2IAK_1|Chain A|Bullous pemphigoid antigen 1, isoform 5|Mus musculus (10090)
>9IQR_1|Chain A|Muscarinic toxin 3|Dendroaspis angusticeps (8618)
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 \(w=f(c)\)
6VBI , Knot 140 325 0.83 40 202 305 
EETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQ
2IAK , Knot 102 224 0.82 40 146 216 
KLMQIRKPLLKSSLLDQNLTEEEVNMKFVQDLLNWVDEMQVQLDRTEWGSDLPSVESHLENHKNVHRAIEEFESSLKEAKISEIQMTAPLKLSYTDKLHRLESQYAKLLNTSRNQERHLDTLHNFVTRATNELIWLNEKEESEVAYDWSERNSSVARKKSYHAELMRELEQKEESIKAVQEIAEQLLLENHPARLTIEAYRAAMQTQWSWILQLCQCVEQHIQE
9IQR , Knot 39 65 0.83 38 58 63 
LTCVTKNTIFGITTENCPAGQNLCFKRWHYVIPRYTEITRGCAATCPIPENYDSIHCCKTDKCNE

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 \(c\).

\(|P_{f(6VBI_1)}(2) \setminus P_{f(2IAK_1)}(2)|=112\), \(|P_{f(2IAK_1)}(2) \setminus P_{f(6VBI_1)}(2)|=56\). 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 1:0000010011111110100101001010010100100110010110010110010100011001110100000001100010011001001111101101000100101111111110001000110000100000111010000110000100011110011001101101000000101100111100111010001011011000010100100001111111010010110011110001101110011001000000101010011000000011010111101101010011001000011110100000001011100
Pair \(Z_2\) Length of longest common subsequence
6VBI_1,2IAK_1 168 3
6VBI_1,9IQR_1 206 2
2IAK_1,9IQR_1 160 3

Newick tree

 
[
	6VBI_1:98.20,
	[
		2IAK_1:80,9IQR_1:80
	]:18.20
]

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 \((0.85)(0.8)(\frac{549 }{\log_{20} 549}-\frac{224}{\log_{20}224})=92.9\)
Status Protein1 Protein2 d d1/2
Query variables 6VBI_1 2IAK_1 117 98.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]