CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2OEL_1 8HSN_1 2XZI_1 Letter Amino acid
4 4 10 W Tryptophan
7 32 24 N Asparagine
0 3 1 C Cysteine
40 32 45 G Glycine
20 17 14 F Phenylalanine
13 36 28 S Serine
17 35 30 T Threonine
9 8 13 Y Tyrosine
51 40 33 A Alanine
31 10 13 E Glutamic acid
23 32 18 I Isoleucine
52 27 24 L Leucine
22 12 18 K Lycine
5 4 5 M Methionine
10 14 6 Q Glutamine
26 13 30 R Arginine
26 21 28 D Aspartic acid
7 17 5 H Histidine
21 14 22 P Proline
29 29 19 V Valine 

2OEL_1|Chains A, B|2,3-diketo-5-methylthiopentyl-1-phosphate enolase|Geobacillus kaustophilus (1462)
>8HSN_1|Chains A, B, C|Fructotransferase|Streptomyces peucetius subsp. caesius ATCC 27952 (316280)
>2XZI_1|Chains A, B|EXTRACELLULAR SIALIDASE/NEURAMINIDASE, PUTATIVE|ASPERGILLUS FUMIGATUS (330879)
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 \(w=f(c)\)
2OEL , Knot 164 413 0.79 38 194 377 
MSAVMATYLLHDETDIRKKAEGIALGLTIGTWTDLPALEQEQLRKHKGEVVAIEELGESERVNAYFGKRLKRAIVKIAYPTVNFSADLPALLVTTFGKLSLDGEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVHNRPLLMSIFKGMIGRDLAYLTSELKKQALGGVDLVKDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGKTFALKDKAKRAAELGADVLLFNVFAYGLDVLQALREDEEIAVPIMAHPAFSGAVTPSEFYGVAPSLWLGKLLRLAGADFVLFPSPYGSVALEREQALGIARALTDDQEPFARAFPVPSAGIHPGLVPLIIRDFGLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGVVEVEA
8HSN , Knot 160 400 0.80 40 205 367 
MADTVYDVTTWAGATVSPYVDIGAVINQIIADIKSKQTTQTTRPGAVIYIPPGHYDLLTRVVIDVSFLQIKGAGHGFLSEAIRDESQTGSWVETLPGASHIRVRNNDGHNEAFLVSRTGAPATVGRLNSIVFQDFCLDGVNASKPYLPGNGKTGISFQSDNDAVRIEGMGFVYLAHALIIKGADAPNITNNFIAECGSSIELTGASQVAKITNNFLISAWAGYSIFAENAEGLQISGNTILWACNITLSSGNRASITSNKLLSNFPSQIALLNNSSENLISANHFRRVHGDGTSTRFDDKFGMVHIAGNKNTVTGNQFSFDVPSQNITPAGQDPTIVLVKSGDNNYLASNHITSNVAAKVVLDASTTATRVLHSATTAQLDALTTNHFMVATPSHHHHHH
2XZI , Knot 162 386 0.83 40 208 360 
INDPAKSAAPYHDEFPLFRSANMASPDKLSTGIGFHSFRIPAVVRTTTGRILAFAEGRRHTNQDFGDINLVYKRTKTTANNGASPSDWEPLREVVGSGAGTWGNPTPVVDDDNTIYLFLSWNGATYSQNGKDVLPDGTVTKKIDSTWEGRRHLYLTESRDDGNTWSKPVDLTKELTPDGWAWDAVGPGNGIRLTTGELVIPAMGRNIIGRGAPGNRTWSVQRLSGAGAEGTIVQTPDGKLYRNDRPSQKGYRMVARGTLEGFGAFAPDAGLPDPACQGSVLRYNSDAPARTIFLNSASGTSRRAMRVRISYDADAKKFNYGRKLEDAKVSGAGHEGGYSSMTKTGDYKIGALVESDFFNDGTGKNSYRAIIWRRFNLSWILNGPNN

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 \(c\).

\(|P_{f(2OEL_1)}(2) \setminus P_{f(8HSN_1)}(2)|=70\), \(|P_{f(8HSN_1)}(2) \setminus P_{f(2OEL_1)}(2)|=81\). 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 1:10111100110000010001011111101101001111000010000101111001100001010110010011101101010101011111100110101010101101011001000111101110110001110001111011011110011010001000111110110000111000111100010010111001000010001011010100111000100110111011110111011011011000001111111011101110100101111011110110111101111101010111000011111011000001110111110111011111111001110011011111010101111110110111011111011011110001100110011110101
Pair \(Z_2\) Length of longest common subsequence
2OEL_1,8HSN_1 151 3
2OEL_1,2XZI_1 164 3
8HSN_1,2XZI_1 131 4

Newick tree

 
[
	2OEL_1:82.78,
	[
		8HSN_1:65.5,2XZI_1:65.5
	]:17.28
]

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 \((0.85)(0.8)(\frac{813 }{\log_{20} 813}-\frac{400}{\log_{20}400})=111.\)
Status Protein1 Protein2 d d1/2
Query variables 2OEL_1 8HSN_1 138 135.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]