CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6IJN_1 9JQB_1 5OQH_1 Letter Amino acid
11 12 13 N Asparagine
4 3 9 C Cysteine
18 7 51 G Glycine
26 6 15 I Isoleucine
19 6 24 R Arginine
18 6 11 F Phenylalanine
31 12 27 S Serine
21 7 28 T Threonine
6 9 21 Y Tyrosine
24 13 25 A Alanine
27 15 33 E Glutamic acid
23 10 19 H Histidine
7 5 9 M Methionine
3 1 11 W Tryptophan
30 6 22 V Valine
25 15 20 D Aspartic acid
9 10 18 Q Glutamine
41 22 30 L Leucine
22 13 20 K Lycine
11 3 25 P Proline 

6IJN_1|Chain A|Adenosine/AMP deaminase family protein|Arabidopsis thaliana (3702)
>9JQB_1|Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X|Ferritin heavy chain|Homo sapiens (9606)
>5OQH_1|Chains A, B|Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain|Mus musculus (10090)
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 \(w=f(c)\)
6IJN , Knot 156 376 0.82 40 208 356 
MGSSHHHHHHHHLEVLFQGPHMEWIQSLPKIELHAHLNGSIRDSTLLELARVLGEKGVIVFADVEHVIQKNDRSLVEVFKLFDLIHKLTTDHKTVTRITREVVEDFALENVVYLELRTTPKRSDSIGMSKRSYMEAVIQGLRSVSEVDIDFVTASDSQKLHNAGDGIGRKKIYVRLLLSIDRRETTESAMETVKLALEMRDVGVVGIDLSGNPLVGEWSTFLPALQYAKDNDLHITLHCGEVPNPKEIQAMLDFKPHRIGHACFFKDEDWTKLKSFRIPVEICLTSNIVTKSISSIDIHHFADLYNAKHPLILCTNDFGVFSTSLSNEYALAVRSLGLSKSETFALARAAIDATFAEDEVKQQLRFIFDSASPEHV
9JQB , Knot 88 183 0.83 42 138 177 
MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEXEHAXKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSDNES
5OQH , Knot 174 431 0.81 40 231 386 
SIINFEKLGCGASGGGGSGGGGSIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDMGGGGSGGGGSGGGGSGGGGSGPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYWERETQAAKGNEQSFRVDLRTLLGCYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDGCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLLRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGTFQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPPPSTVSNHHHHHH

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 \(c\).

\(|P_{f(6IJN_1)}(2) \setminus P_{f(9JQB_1)}(2)|=119\), \(|P_{f(9JQB_1)}(2) \setminus P_{f(6IJN_1)}(2)|=49\). 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 1:1100000000001011101101011001101010101010100001101101110011111101001100000011011011011001000000100100011001110011010100010000011100000101110110010010101101000001001101110001010111010000000011001011101001111110101011110100111110010000101010010110100101110101001101011000010010010111010100011000100101001101001001111000011110001000011110011100000111101110101100010001011100101001
Pair \(Z_2\) Length of longest common subsequence
6IJN_1,9JQB_1 168 4
6IJN_1,5OQH_1 151 6
9JQB_1,5OQH_1 203 3

Newick tree

 
[
	9JQB_1:98.34,
	[
		6IJN_1:75.5,5OQH_1:75.5
	]:22.84
]

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 \((0.85)(0.8)(\frac{559 }{\log_{20} 559}-\frac{183}{\log_{20}183})=108.\)
Status Protein1 Protein2 d d1/2
Query variables 6IJN_1 9JQB_1 137 101
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]