CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5PFV_1 1FJE_1 9ITR_1 Letter Amino acid
5 0 2 R Arginine
12 0 0 D Aspartic acid
8 0 5 F Phenylalanine
8 0 9 V Valine
6 0 2 P Proline
4 6 10 A Alanine
14 0 0 K Lycine
6 0 2 M Methionine
11 0 1 S Serine
8 0 3 T Threonine
6 0 3 N Asparagine
2 7 0 C Cysteine
2 0 2 Q Glutamine
9 0 4 E Glutamic acid
6 7 13 G Glycine
8 0 0 H Histidine
4 0 11 I Isoleucine
13 0 8 L Leucine
2 0 0 W Tryptophan
4 0 1 Y Tyrosine 

5PFV_1|Chain A|Bromodomain adjacent to zinc finger domain protein 2B|Homo sapiens (9606)
>1FJE_1|Chain A|SNRE RNA|null
>9ITR_1|Chains A[auth H], B[auth I], C[auth J], D[auth K], E[auth L], F[auth M], G[auth N], H[auth O], I[auth P], J[auth Q]|ATP synthase subunit c|Chloroflexus aurantiacus J-10-fl (324602)
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 \(w=f(c)\)
5PFV , Knot 66 138 0.78 40 109 129 
MHHHHHHSSGVDLGTENLYFQSMSVKKPKRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTFKVS
1FJE , Knot 9 22 0.42 8 11 15 
GGCCGAAAUCCCGAAGUAGGCC
9ITR , Knot 37 76 0.70 30 55 70 
MEGLNLVATALAVGLGAIGPGVGIGIIVSGAVQAIGRNPEIENRVVTYMFIGIAFTEALAIFGLVIAFLIGFGVLQ

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 \(c\).

\(|P_{f(5PFV_1)}(2) \setminus P_{f(1FJE_1)}(2)|=108\), \(|P_{f(1FJE_1)}(2) \setminus P_{f(5PFV_1)}(2)|=10\). 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 1:100000000110110001010010100100000001110011100100000111111110101111000110011010010001001001010011101011100000100000011011001000100010001010
Pair \(Z_2\) Length of longest common subsequence
5PFV_1,1FJE_1 118 2
5PFV_1,9ITR_1 132 3
1FJE_1,9ITR_1 64 2

Newick tree

 
[
	5PFV_1:69.88,
	[
		1FJE_1:32,9ITR_1:32
	]:37.88
]

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 \((0.85)(0.8)(\frac{160 }{\log_{20} 160}-\frac{22}{\log_{20}22})=49.7\)
Status Protein1 Protein2 d d1/2
Query variables 5PFV_1 1FJE_1 65 36.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]