CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5AEQ_1 1JHF_1 4FVY_1 Letter Amino acid
11 6 25 T Threonine
7 1 16 Y Tyrosine
7 15 22 R Arginine
1 0 11 C Cysteine
17 16 25 E Glutamic acid
5 5 11 M Methionine
10 13 18 Q Glutamine
17 11 27 K Lycine
15 6 19 F Phenylalanine
9 9 26 S Serine
10 16 20 A Alanine
9 13 23 I Isoleucine
15 22 36 L Leucine
7 9 23 P Proline
2 1 13 W Tryptophan
12 19 24 V Valine
8 6 18 N Asparagine
16 13 26 D Aspartic acid
12 16 25 G Glycine
0 5 14 H Histidine

5AEQ_1|Chains A, B|NEURONAL CALCIUM SENSOR 1|RATTUS NORVEGICUS (10116)
>1JHF_1|Chains A, B|LEXA REPRESSOR|Escherichia coli (562)
>4FVY_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 \(w=f(c)\)
5AEQ , Knot 92 190 0.84 38 139 185
MGKSNSKLKPEVVEELTRKTYFTEKEVQQWYKGFIKDCPSGQLDAAGFQKIYKQFFPFGDPTKFATFVFNVFDENKDGRIEFSEFIQALSVTSRGTLDEKLRWAFKLYDLDNDGYITRNEMLDIVDAIYQMVGNTVELPEEENTPEKRVDRIFAMMDKNADGKLTLQEFQEGSKADPSIVQALSLYDGLV
1JHF , Knot 95 202 0.83 38 137 188
MKALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVGRVAADEPLLAQQHIEGHYQVDPSLFKPNADFLLRVSGMSMKDIGIMDGDLLAVHKTQDVRNGQVVVARIDDEVTVKRLKKQGNKVELLPENSEFKPIVVDLRQQSFTIEGLAVGVIRNGDWL
4FVY , 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 \(c\).

\(|P_{f(5AEQ_1)}(2) \setminus P_{f(1JHF_1)}(2)|=74\), \(|P_{f(1JHF_1)}(2) \setminus P_{f(5AEQ_1)}(2)|=72\). 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 1:1100000101011001000001000010010011100010101011110010001111101001101110110000010101001101101000101000101110100100010100001101101100111001011000001000100111110001010101001001001010110110100111
Pair \(Z_2\) Length of longest common subsequence
5AEQ_1,1JHF_1 146 3
5AEQ_1,4FVY_1 177 4
1JHF_1,4FVY_1 189 3

Newick tree

 
[
	4FVY_1:96.94,
	[
		5AEQ_1:73,1JHF_1:73
	]:23.94
]

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 \((0.85)(0.8)(\frac{392 }{\log_{20} 392}-\frac{190}{\log_{20}190})=59.9\)
Status Protein1 Protein2 d d1/2
Query variables 5AEQ_1 1JHF_1 73 71.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]