CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6OYW_1 3RMD_1 1EXA_1 Letter Amino acid
25 70 20 E Glutamic acid
22 74 15 I Isoleucine
13 48 5 V Valine
10 44 4 N Asparagine
5 8 6 C Cysteine
7 17 3 H Histidine
15 43 16 P Proline
12 38 19 T Threonine
18 57 15 D Aspartic acid
11 46 15 R Arginine
26 51 13 G Glycine
27 70 13 K Lycine
18 55 12 S Serine
2 12 1 W Tryptophan
13 53 5 Y Tyrosine
16 52 15 A Alanine
26 64 37 L Leucine
6 25 12 M Methionine
12 48 10 F Phenylalanine
10 31 10 Q Glutamine 

6OYW_1|Chains A, B, C, D|Mitogen-activated protein kinase kinase kinase 5|Homo sapiens (9606)
>3RMD_1|Chains A, B, C, D|DNA polymerase|Enterobacteria phage RB69 (12353)
>1EXA_1|Chain A|RETINOIC ACID RECEPTOR GAMMA-2|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 \(w=f(c)\)
6OYW , Knot 132 294 0.85 40 189 282 
GRSTEEGDCESDLLEYDYEYDENGDRVVLGKGTYGIVYAGRDLSNQVRIAIKEIPERDSRYSQPLHEEIALHKHLKHKNIVQYLGSFSENGFIKIFMEQVPGGSLSALLRSKWGPLKDNEQTIGFYTKQILEGLKYLHDNQIVHRDIKGDNVLINTYSGVLKISDFGTSKRLAGINPCTEEFTGTLQYMAPEIIDKGPRGYGKAADIWSLGCTIIEMATGKPPFYELGEPQAAMFKVGMFKVHPEIPESMSAEAKAFILKCFEPDPDKRACANDLLVDEFLKVSSKKKKTQPKL
3RMD , Knot 338 906 0.84 40 320 827 
MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDFHHH
1EXA , Knot 112 246 0.83 40 165 239 
DSYELSPQLEELITKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLENPEMFE

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 \(c\).

\(|P_{f(6OYW_1)}(2) \setminus P_{f(3RMD_1)}(2)|=21\), \(|P_{f(3RMD_1)}(2) \setminus P_{f(6OYW_1)}(2)|=152\). 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 1:100000100000110000000001001111010011101100100010111001100000000110001110001000011001101000111011100111101011100011110000001110000110110010000110001010011100001110100110000111101000010101001110110011010101101101100110110101110011010111101111010101100101010111100101010001010011100110100000000101
Pair \(Z_2\) Length of longest common subsequence
6OYW_1,3RMD_1 173 5
6OYW_1,1EXA_1 156 3
3RMD_1,1EXA_1 185 4

Newick tree

 
[
	3RMD_1:93.08,
	[
		6OYW_1:78,1EXA_1:78
	]:15.08
]

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 \((0.85)(0.8)(\frac{1200 }{\log_{20} 1200}-\frac{294}{\log_{20}294})=239.\)
Status Protein1 Protein2 d d1/2
Query variables 6OYW_1 3RMD_1 306 201
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]