CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5JXE_1 3ERM_1 4FHW_1 Letter Amino acid
1 2 8 H Histidine
2 2 22 I Isoleucine
9 11 40 L Leucine
7 3 22 F Phenylalanine
9 15 19 A Alanine
10 4 19 R Arginine
2 0 4 C Cysteine
5 2 20 G Glycine
7 5 17 V Valine
5 1 10 Q Glutamine
2 3 6 M Methionine
8 2 16 P Proline
9 6 14 T Threonine
1 0 2 W Tryptophan
2 2 18 Y Tyrosine
13 7 32 S Serine
7 5 12 N Asparagine
6 6 20 D Aspartic acid
6 10 22 E Glutamic acid
3 5 26 K Lycine 

5JXE_1|Chains A, B|Programmed cell death protein 1|Homo sapiens (9606)
>3ERM_1|Chains A, B, C, D, E|uncharacterized conserved protein|Pseudomonas syringae pv. tomato (323)
>4FHW_1|Chain A|Poly(A) RNA polymerase protein cid1|Schizosaccharomyces pombe (284812)
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 \(w=f(c)\)
5JXE , Knot 61 114 0.84 40 96 110 
NPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTE
3ERM , Knot 49 91 0.81 36 71 87 
SNAMAVETLYRSTRDLETTFVDRKLADAHDQMLELAELLTDVLIKNVPGLSEKHAEDASIYMAKNRAVFAAAFKNNATALSELSEPAESEG
4FHW , Knot 154 349 0.86 40 208 332 
GSHMSYQKVPNSHKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSATEHTGSADQIIKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEA

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 \(c\).

\(|P_{f(5JXE_1)}(2) \setminus P_{f(3ERM_1)}(2)|=69\), \(|P_{f(3ERM_1)}(2) \setminus P_{f(5JXE_1)}(2)|=44\). 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 1:011010111111001001010001000000111010010100000011111000001100001010011010010101101000001001011101110101000101010100
Pair \(Z_2\) Length of longest common subsequence
5JXE_1,3ERM_1 113 3
5JXE_1,4FHW_1 190 3
3ERM_1,4FHW_1 187 3

Newick tree

 
[
	4FHW_1:10.83,
	[
		5JXE_1:56.5,3ERM_1:56.5
	]:47.33
]

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 \((0.85)(0.8)(\frac{205 }{\log_{20} 205}-\frac{91}{\log_{20}91})=37.3\)
Status Protein1 Protein2 d d1/2
Query variables 5JXE_1 3ERM_1 47 41.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]