CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7OKD_1 3AKJ_1 7SQY_1 Letter Amino acid
7 16 22 E Glutamic acid
5 15 19 Y Tyrosine
13 27 29 D Aspartic acid
5 9 5 C Cysteine
3 11 11 H Histidine
9 23 17 I Isoleucine
8 19 17 F Phenylalanine
10 14 36 V Valine
8 14 30 A Alanine
9 10 17 R Arginine
8 29 20 N Asparagine
9 18 36 S Serine
0 2 3 W Tryptophan
3 14 27 P Proline
7 18 32 T Threonine
5 10 12 Q Glutamine
6 12 41 G Glycine
17 29 44 L Leucine
6 27 26 K Lycine
6 8 9 M Methionine 

7OKD_1|Chain A|B-cell lymphoma 6 protein|Homo sapiens (9606)
>3AKJ_1|Chains A, B|CtkA|Helicobacter pylori (85963)
>7SQY_1|Chains A, B, C|Citrus Sudden Death-associated Virus Capsid Protein,Green fluorescent protein,Citrus Sudden Death-associated Virus Capsid Protein|Citrus sudden death-associated virus (312008)
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 \(w=f(c)\)
7OKD , Knot 73 144 0.84 38 109 140 
GPGLDYKDDDDKENLYFQGADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKASE
3AKJ , Knot 141 325 0.83 40 189 307 
MPTIDFTFCEINPKKGFGGANGNKISLFYNNELYMVKFPPKPSTHKEMSYTNGCFSEYVACHIVNSLGLKVQETLLGTYKNKIVVACKDFTTHQYELVDFLSLKNTMIELEKSGKDTNLNDVLYAIDNQHFIEPKVLKCFFWDMFVADTLLGNFDRHNGNWGFLRASNSKEYQIAPIFDCGSCLYPQADDVVCQKVLSNIDELNARIYNFPQSILKDDNDKKINYYDFLTQTNNKDCLDALLRIYPRIDMNKIHSIIDNTPFMSEIHKEFLHTMLDERKSKIIDVAHTRAIELSLQHKQAHSNPYDNADDLDNSNEYTPTPKRRR
7SQY , Knot 188 453 0.84 40 234 420 
MQSDTLLPLTGGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKLTGGFSMASDAQAGPAPSRDDRVDRQPRLPAAPRVAEVGLNAPSVDYPFQWVVASYDGSEAKNLSDDLSGSATLTKVMANYRHAELTSVELEVCPLAAAFSKPISVSAVWTIASISPASASETSYYGGRLFTVGGPVLMSSTTHLPADLTRLNPVLKGPVKYTDCPRFSYSVYSNGGTKGTNLCTIILRGVVRLSGPSGNLLA

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 \(c\).

\(|P_{f(7OKD_1)}(2) \setminus P_{f(3AKJ_1)}(2)|=55\), \(|P_{f(3AKJ_1)}(2) \setminus P_{f(7OKD_1)}(2)|=135\). 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 1:111100000000001010110001010001001110100100001100111110000101000111100111001100010001011010101010110111011000010100101111110110101001100000110100
Pair \(Z_2\) Length of longest common subsequence
7OKD_1,3AKJ_1 190 4
7OKD_1,7SQY_1 201 3
3AKJ_1,7SQY_1 173 4

Newick tree

 
[
	7OKD_1:10.27,
	[
		3AKJ_1:86.5,7SQY_1:86.5
	]:14.77
]

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 \((0.85)(0.8)(\frac{469 }{\log_{20} 469}-\frac{144}{\log_{20}144})=96.3\)
Status Protein1 Protein2 d d1/2
Query variables 7OKD_1 3AKJ_1 123 87
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]