CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1MNY_1 6FKA_1 6HSM_1 Letter Amino acid
9 4 8 D Aspartic acid
6 23 14 G Glycine
0 16 3 M Methionine
2 31 1 F Phenylalanine
1 5 3 W Tryptophan
1 14 0 N Asparagine
0 12 5 C Cysteine
2 12 5 Q Glutamine
12 17 8 E Glutamic acid
5 22 5 I Isoleucine
7 27 10 T Threonine
4 29 27 A Alanine
8 28 17 L Leucine
3 20 12 P Proline
6 15 8 S Serine
4 18 2 Y Tyrosine
5 31 16 V Valine
3 7 9 R Arginine
6 6 8 H Histidine
10 11 5 K Lycine 

1MNY_1|Chain A|cytochrome b5|Rattus norvegicus (10116)
>6FKA_1|Chain A|Rhodopsin|Bos taurus (9913)
>6HSM_1|Chains A, B, C, D, E, F, G, H|Rrf2 family transcriptional regulator|Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (953739)
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 \(w=f(c)\)
1MNY , Knot 47 94 0.75 36 76 91 
DKDVKYYTLEEIQKHKDSKSTWVILHHKVYDLTKFLEEHPGGEEVLREQAGGDATENFEDVGHSTDARELSKTYIIGELHPDDRSKIAKPSETL
6FKA , Knot 154 349 0.86 42 215 337 
XMCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA
6HSM , Knot 77 166 0.79 38 117 159 
MKLSGGVEWALHCCVVLTAASRPVPAARLAELHDVSPSYLAKQMQALSRAGLVRSVQGKTGGYVLTRPAVEITLLDVVQAVDGPDPAFVCTEIRQRGPLATPPEKCTKACPIARAMGAAEAAWRASLAATTIADLVATVDDESGPDALPGVGAWLIEGLGHHHHHH

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 \(c\).

\(|P_{f(1MNY_1)}(2) \setminus P_{f(6FKA_1)}(2)|=34\), \(|P_{f(6FKA_1)}(2) \setminus P_{f(1MNY_1)}(2)|=173\). 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 1:0001000010010000000001111000100100110001110011000111010001001100001001000011101010000011010001
Pair \(Z_2\) Length of longest common subsequence
1MNY_1,6FKA_1 207 3
1MNY_1,6HSM_1 137 3
6FKA_1,6HSM_1 186 3

Newick tree

 
[
	6FKA_1:10.50,
	[
		1MNY_1:68.5,6HSM_1:68.5
	]:38.00
]

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 \((0.85)(0.8)(\frac{443 }{\log_{20} 443}-\frac{94}{\log_{20}94})=105.\)
Status Protein1 Protein2 d d1/2
Query variables 1MNY_1 6FKA_1 139 87
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: