CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8OKG_1 6QYM_1 4FVD_1 Letter Amino acid
12 18 8 Q Glutamine
12 3 6 H Histidine
17 10 4 P Proline
19 19 14 S Serine
13 13 6 T Threonine
18 22 13 V Valine
13 21 11 A Alanine
19 14 8 D Aspartic acid
23 20 3 K Lycine
1 2 5 C Cysteine
13 29 7 E Glutamic acid
8 18 5 I Isoleucine
26 23 12 L Leucine
11 14 4 F Phenylalanine
7 3 3 W Tryptophan
7 16 9 R Arginine
9 28 7 N Asparagine
22 11 17 G Glycine
2 8 2 M Methionine
8 17 8 Y Tyrosine 

8OKG_1|Chain A|Carbonic anhydrase 2|Homo sapiens (9606)
>6QYM_1|Chains A[auth 0a], B[auth 0b], C[auth 0c], D[auth 0d], E[auth 0e], F[auth 0f], G[auth 0g], H[auth 0h], I[auth 0i], J[auth 0j], K[auth 0k], L[auth 0l]|Portal protein|Bacillus phage phi29 (10756)
>4FVD_1|Chain A|2A proteinase|Human enterovirus 71 (39054)
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 \(w=f(c)\)
8OKG , Knot 112 260 0.79 40 171 249 
MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
6QYM , Knot 136 309 0.84 40 195 296 
MARKRSNTYRSINEIQRQKRNRWFIHYLNYLQSLAYQLFEWENLPPTINPSFLEKSIHQFGYVGFYKDPVISYIACNGALSGQRDVYNQATVFRAASPVYQKEFKLYNYRDMKEEDMGVVIYNNDMAFPTTPTLELFAAELAELKEIISVNQNAQKTPVLIRANDNNQLSLKQVYNQYEGNAPVIFAHEALDSDSIEVFKTDAPYVVDKLNAQKNAVWNEMMTFLGIKNANLEKKERMVTDEVSSNDEQIESSGTVFLKSREEACEKINELYGLNVKVKFRYDIVEQMRRELQQIENVSRGTSDGETNE
4FVD , Knot 73 152 0.80 40 117 146 
GSGKFGQQSGAIYVGNFRVVNRHLATHNDWANLVWEDSSRDLLVSSTTAQGCDTIARCNCQTGVYYCNSRRKHYPVSFSKPSLIYVEASEYYPARYQSHLMLAQGHSEPGDAGGILRCQHGVVGIVSTGGNGLVGFADVRDLLWLDEEAMEQ

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 \(c\).

\(|P_{f(8OKG_1)}(2) \setminus P_{f(6QYM_1)}(2)|=78\), \(|P_{f(6QYM_1)}(2) \setminus P_{f(8OKG_1)}(2)|=102\). 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 1:10001101000110010001111010000110100001000101011010000100101100100101010000001110111101000110101011010101000010000011010110100001011011001011111111101101011100110110010001001010010101111001001001101001111001011110011010000110100101010101001110010110110000101010
Pair \(Z_2\) Length of longest common subsequence
8OKG_1,6QYM_1 180 4
8OKG_1,4FVD_1 174 3
6QYM_1,4FVD_1 190 3

Newick tree

 
[
	6QYM_1:94.30,
	[
		8OKG_1:87,4FVD_1:87
	]:7.30
]

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 \((0.85)(0.8)(\frac{569 }{\log_{20} 569}-\frac{260}{\log_{20}260})=87.4\)
Status Protein1 Protein2 d d1/2
Query variables 8OKG_1 6QYM_1 110 101.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]