CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2ZZT_1 1XOY_1 5DAD_1 Letter Amino acid
9 2 5 R Arginine
0 9 10 Q Glutamine
12 15 8 E Glutamic acid
11 13 6 K Lycine
6 1 9 M Methionine
4 9 7 F Phenylalanine
4 6 6 T Threonine
10 3 5 H Histidine
7 9 6 I Isoleucine
3 8 4 P Proline
0 1 0 W Tryptophan
10 8 6 D Aspartic acid
0 2 3 C Cysteine
7 9 7 G Glycine
6 15 11 L Leucine
2 8 12 A Alanine
3 10 4 N Asparagine
1 18 13 S Serine
2 4 4 Y Tyrosine
10 11 14 V Valine 

2ZZT_1|Chain A|Putative uncharacterized protein|Thermotoga maritima (2336)
>1XOY_1|Chain A|hypothetical protein At3g04780.1|Arabidopsis thaliana (3702)
>5DAD_1|Chain A|Kelch-like ECH-associated protein 1|Homo sapiens (9606)
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 \(w=f(c)\)
2ZZT , Knot 53 107 0.77 34 83 100 
MDGMKRTELDMYDDIFAVLERFPNVHNPHRVRIRRVGTKYFIEMDIEVDGKMSVKDAHELTVKIRKEMLKRRDDIEDVTIHVEPLGNVEEEGFGLKKGEKKHHHHHH
1XOY , Knot 78 161 0.82 40 122 156 
SSAESASQIPKGQVDLLDFIDWSGVECLNQSSSHSLPNALKQGYREDEGLNLESDADEQLLIYIPFNQVIKLHSFAIKGPEEEGPKTVKFFSNKEHMCFSNVNDFPPSDTAELTEENLKGKPVVLKYVKFQNVRSLTIFIEANQSGSEVTKVQKIALYGST
5DAD , Knot 72 140 0.84 38 116 137 
GSHMASNRTFSYTLEDHTKQAFGIMNELRLSQQLCDVTLQVKYQDAPAAQFMAHKVVLASSSPVFKAMFTNGLREQGMEVVSIEGIHPKVMERLIEFAYTASISMGEKCVLHVMNGAVMYQIDSVVRACSDFLVQQLDPS

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 \(c\).

\(|P_{f(2ZZT_1)}(2) \setminus P_{f(1XOY_1)}(2)|=50\), \(|P_{f(1XOY_1)}(2) \setminus P_{f(2ZZT_1)}(2)|=89\). 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 1:10110000101000111110011010010010100110001101010101010100100101010001100000100101010111010001111001000000000
Pair \(Z_2\) Length of longest common subsequence
2ZZT_1,1XOY_1 139 4
2ZZT_1,5DAD_1 141 3
1XOY_1,5DAD_1 152 3

Newick tree

 
[
	5DAD_1:74.52,
	[
		2ZZT_1:69.5,1XOY_1:69.5
	]:5.02
]

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 \((0.85)(0.8)(\frac{268 }{\log_{20} 268}-\frac{107}{\log_{20}107})=51.0\)
Status Protein1 Protein2 d d1/2
Query variables 2ZZT_1 1XOY_1 63 51.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]