CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6NXL_1 2FNA_1 1XCS_1 Letter Amino acid
3 22 0 R Arginine
0 2 2 C Cysteine
6 35 0 E Glutamic acid
8 32 0 I Isoleucine
6 34 0 K Lycine
1 5 0 M Methionine
3 11 0 P Proline
2 19 0 N Asparagine
7 7 0 Q Glutamine
0 2 0 H Histidine
2 21 0 F Phenylalanine
1 4 0 W Tryptophan
6 19 0 D Aspartic acid
7 20 2 G Glycine
9 49 0 L Leucine
5 21 0 S Serine
6 9 1 T Threonine
1 17 0 Y Tyrosine
4 12 0 V Valine
3 16 1 A Alanine 

6NXL_1|Chains A, B, C, D, E, F, G, H|Polyubiquitin-B|Homo sapiens (9606)
>2FNA_1|Chains A, B|Conserved hypothetical protein|Sulfolobus solfataricus (273057)
>1XCS_1|Chains A, B|5'-D(*CP*GP*TP*AP*CP*G)-3'|
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 \(w=f(c)\)
6NXL , Knot 45 80 0.82 36 66 77 
GSGGSGMQIFVDTVQWKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESALILLLTLR
2FNA , Knot 149 357 0.81 40 193 337 
GMLFDTSPKDNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDYEVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAKKLILKEFENFLHGREIARKRYLNIMRTLSKCGKWSDVKRALELEEGIEISDSEIYNYLTQLTKHSWIIKEGEKYCPSEPLISLAFS
1XCS , Knot 5 6 0.49 8 4 4 
CGTACG

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 \(c\).

\(|P_{f(6NXL_1)}(2) \setminus P_{f(2FNA_1)}(2)|=21\), \(|P_{f(2FNA_1)}(2) \setminus P_{f(6NXL_1)}(2)|=148\). 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 1:10110110111001010010101010001001010100001111000011111001001001000010000111111010
Pair \(Z_2\) Length of longest common subsequence
6NXL_1,2FNA_1 169 4
6NXL_1,1XCS_1 70 1
2FNA_1,1XCS_1 195 2

Newick tree

 
[
	2FNA_1:10.38,
	[
		6NXL_1:35,1XCS_1:35
	]:68.38
]

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 \((0.85)(0.8)(\frac{437 }{\log_{20} 437}-\frac{80}{\log_{20}80})=109.\)
Status Protein1 Protein2 d d1/2
Query variables 6NXL_1 2FNA_1 136 81.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: