CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8AQR_1 6EJA_1 4FZO_1 Letter Amino acid
1 29 4 Y Tyrosine
3 29 0 Q Glutamine
2 27 6 I Isoleucine
3 18 3 M Methionine
3 47 6 S Serine
1 37 1 F Phenylalanine
3 49 6 R Arginine
3 43 9 D Aspartic acid
7 35 12 E Glutamic acid
4 44 4 G Glycine
4 48 3 V Valine
0 14 2 C Cysteine
2 31 2 H Histidine
10 71 10 L Leucine
3 42 3 T Threonine
1 19 0 W Tryptophan
1 51 4 A Alanine
1 32 2 N Asparagine
4 37 5 K Lycine
2 48 0 P Proline 

8AQR_1|Chains A, B, C, D, E, F|AerJ|Microcystis aeruginosa NIES-98 (267869)
>6EJA_1|Chain A|Xylosyltransferase 1|Homo sapiens (9606)
>4FZO_1|Chains A, B|uranyl binding protein|Methanothermobacter thermautotrophicus (187420)
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 \(w=f(c)\)
8AQR , Knot 35 58 0.81 38 51 56 
GSMKTVEFLSDLNHLGVTIWMEGDKLRYRSPQGVMTPDLLEQLKEHKEELIVLLREQA
6EJA , Knot 298 751 0.87 40 326 709 
APLVHHHHHHALDENLYFQGALADVSRPPHARKTGGSSPETKYDQPPKCDISGKEAISALSRAKSKHCRQEIGETYCRHKLGLLMPEKVTRFCPLEGKANKNVQWDEDSVEYMPANPVRIAFVLVVHGRASRQLQRMFKAIYHKDHFYYIHVDKRSNYLHRQVLQVSRQYSNVRVTPWRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFINLSAADYPIRTNDQLVAFLSRYRDMNFLKSHGRDNARFIRKQGLDRLFLECDAHMWRLGDRRIPEGIAVDGGSDWFLLNRRFVEYVTFSTDDLVTKMKQFYSYTLLPAESFFHTVLENSPHCDTMVDNNLRITNWNRKLGCKCQYKHIVDWCGCSPNDFKPQDFHRFQQTARPTFFARKFEAVVNQEIIGQLDYYLYGNYPAGTPGLRSYWENVYDEPDGIHSLSDVTLTLYHSFARLGLRRAETSLHTDGENSCRYYPMGHPASVHLYFLADRFQGFLIKHHATNLAVSKLETLETWVMPKKVFKIASPPSDFGRLQFSEVGTDWDAKERLFRNFGGLLGPMDEPVGMQKWGKGPNVTVTVIWVDPVNVIAATYDILIESTAEFTHYKPPLNLPLRPGVWTVKILHHWVPVAETKFLVAPLTFSNRQPIKPEEALKLHNGPLRNAYMEQSFQSLNPVLSLPINPAQVEQARRNAASTGTALEGWLDSLVGGMWTAMDICATGPTACPVMQTCSQTAWSSFSPDPKSELGAVKPDGRLR
4FZO , Knot 44 82 0.78 34 68 78 
SNALDCRERIEKDLEDLEKELMEMKSIKLSDDEEAVVERALNYRDDSVYYLEKGDHITSFGCITYAEGLTDSLRMLHRIIEG

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 \(c\).

\(|P_{f(8AQR_1)}(2) \setminus P_{f(6EJA_1)}(2)|=4\), \(|P_{f(6EJA_1)}(2) \setminus P_{f(8AQR_1)}(2)|=279\). 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 1:1010010110010011101110100100001011101011001000000111110001
Pair \(Z_2\) Length of longest common subsequence
8AQR_1,6EJA_1 283 4
8AQR_1,4FZO_1 85 3
6EJA_1,4FZO_1 270 4

Newick tree

 
[
	6EJA_1:15.78,
	[
		8AQR_1:42.5,4FZO_1:42.5
	]:11.28
]

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 \((0.85)(0.8)(\frac{809 }{\log_{20} 809}-\frac{58}{\log_{20}58})=217.\)
Status Protein1 Protein2 d d1/2
Query variables 8AQR_1 6EJA_1 280 150
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: