CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8VSZ_1 7MIC_1 3SVP_1 Letter Amino acid
42 14 26 S Serine
7 3 11 C Cysteine
22 7 25 E Glutamic acid
48 20 36 L Leucine
31 8 19 F Phenylalanine
35 12 25 T Threonine
19 19 20 A Alanine
20 10 26 D Aspartic acid
14 2 18 Q Glutamine
5 5 14 H Histidine
27 4 23 I Isoleucine
17 1 27 K Lycine
10 11 23 P Proline
7 1 13 W Tryptophan
24 11 22 R Arginine
20 11 25 G Glycine
13 1 11 M Methionine
23 2 16 Y Tyrosine
34 9 24 V Valine
22 3 18 N Asparagine 

8VSZ_1|Chains A, B, C, D, E|Gamma-aminobutyric acid receptor subunit pi|Homo sapiens (9606)
>7MIC_1|Chain A|RNA replication protein|Maize rayado fino virus (59749)
>3SVP_1|Chains A, B|Nitric oxide synthase, brain|Rattus norvegicus (10116)
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 \(w=f(c)\)
8VSZ , Knot 186 440 0.85 40 243 411 
MNYSLHLAFVCLSLFTERMCIQGSQFNVEVGRSDKLSLPGFENLTAGYNKFLRPNFGGEPVQIALTLDIASISSISESNMDYTATIYLRQRWMDQRLVFEGNKSFTLDARLVEFLWVPDTYIVESKKSFLHEVTVGNRLIRLFSNGTVLYALRITTTVACNMDLSKYPMDTQTCKLQLESWGYDGNDVEFTWLRGNDSVRGLEHLRLAQYTIERYFTLVTRSQQETGNYTRLVLQFELRRNVLYFILETYVPSTFLVVLSWVSFWISLDSVPARTCIGVTTVLSMTTLMIGSRTSLPNTNCFIKAIDVYLGICFSFVFGALLEYAVAHYSSLQQMAAKDRGTTKEVEEVSITNIINSSISSFKRKISFASIEISSDNVDYSDLTMKTSDKFKFVFREKMGRIVDYFTIQNPSNVDHYSKLLFPLIFMLANVFYWAYYMYF
7MIC , Knot 75 154 0.81 40 112 149 
GPLGSPEPDTARLDADPSASGPVMEFRELQKGAYIEPTGAFLTRARNSVSSSIPYPARAACLLVAVSQATGLPTRTLWAALCANLPDSVLDDGSLATLGLTTDHFAVLARIFSLRCRFVSEHGDVELGLHDATSRFTIRHTPGHFELVADNFSL
3SVP , Knot 186 422 0.88 40 262 411 
CPRFLKVKNWETDVVLTDTLHLKSTLETGCTEHICMGSIMLPSQHTRKPEDVRTKDQLFPLAKEFLDQYYSSIKRFGSKAHMDRLEEVNKEIESTSTYQLKDTELIYGAKHAWRNASRCVGRIQWSKLQVFDARDCTTAHGMFNYICNHVKYATNKGNLRSAITIFPQRTDGKHDFRVWNSQLIRYAGYKQPDGSTLGDPANVQFTEICIQQGWKAPRGRFDVLPLLLQANGNDPELFQIPPELVLEVPIRHPKFDWFKDLGLKWYGLPAVSNMLLEIGGLEFSACPFSGWYMGTEIGVRDYCDNSRYNILEEVAKKMDLDMRKTSSLWKDQALVEINIAVLYSFQSDKVTIVDHHSATESFIKHMENEYRCRGGCPADWVWIVPPMSGSITPVFHQEMLNYRLTPSFEYQPDPWNTHVWKG

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 \(c\).

\(|P_{f(8VSZ_1)}(2) \setminus P_{f(7MIC_1)}(2)|=162\), \(|P_{f(7MIC_1)}(2) \setminus P_{f(8VSZ_1)}(2)|=31\). 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 1:10001011110101100010101001010110000101111001011000110101110110111010110100100001000101010001100011101000101010110111110001100000110010110011011001011011010001100101000110000001010011001001010110100010110010110001000101100000001000011101010001101110001100111110110111010011100011100110100111100001100001101101011101011111110011100001001110001000010010100110001001000101101010000100001010000010111000110110010100100100000111111111101101100101
Pair \(Z_2\) Length of longest common subsequence
8VSZ_1,7MIC_1 193 3
8VSZ_1,3SVP_1 167 4
7MIC_1,3SVP_1 204 3

Newick tree

 
[
	7MIC_1:10.01,
	[
		8VSZ_1:83.5,3SVP_1:83.5
	]:20.51
]

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 \((0.85)(0.8)(\frac{594 }{\log_{20} 594}-\frac{154}{\log_{20}154})=127.\)
Status Protein1 Protein2 d d1/2
Query variables 8VSZ_1 7MIC_1 162 107.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]