CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5WJH_1 3DIQ_1 7RTV_1 Letter Amino acid
17 0 20 N Asparagine
5 0 19 E Glutamic acid
12 0 25 R Arginine
5 47 20 C Cysteine
7 0 31 Q Glutamine
33 68 34 G Glycine
11 0 26 I Isoleucine
8 0 8 K Lycine
5 0 12 M Methionine
9 0 24 P Proline
2 0 8 W Tryptophan
19 0 31 V Valine
33 32 41 A Alanine
4 0 14 H Histidine
14 0 77 L Leucine
6 0 21 F Phenylalanine
36 0 46 S Serine
14 0 26 D Aspartic acid
22 0 34 T Threonine
17 0 23 Y Tyrosine 

5WJH_1|Chain A|Proteinase K|Parengyodontium album (37998)
>3DIQ_1|Chain A|RNA (174-MER)|null
>7RTV_1|Chain A|Protein tweety homolog 2|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 \(w=f(c)\)
5WJH , Knot 120 279 0.80 40 170 266 
AAQTNAPWGLARISSTSPGTSTYYYDESAGQGSCVYVIDTGIEASHPEFEGRAQMVKTYYYSSRDGNGHGTHCAGTVGSRTYGVAKKTQLFGVKVLDDNGSGQYSTIIAGMDFVASDKNNRNCPKGVVASLSLGGGYSSSVNSAAARLQSSGVMVAVAAGNNNADARNYSPASEPSVCTVGASDRYDRRSSFSNYGSVLDIFGPGTDILSTWIGGSTRSISGTSMATPHVAGLAAYLMTLGKTTAASACRYIADTANKGDLSNIPFGTVNLLAYNNYQA
3DIQ , Knot 46 174 0.45 8 16 54 
GGCCGACGGAGGCGCGCCCGAGAUGAGUAGGCUGUCCCAUCAGGGGAGGAAUCGGGGACGGCUGAAAGGCGAGGGCGCCGAAGGGUGCAGAGUUCCUCCCGCUCUGCAUGCCUGGGGGUAUGGGGAAUACCCAUACCACUGUCACGGAGGUCUCUCCGUGGAGAGCCGUCGGUC
7RTV , Knot 214 540 0.83 40 248 496 
PAARVEYIAPWWVVWLHSVPHLGLRLQRVDSTFSPGDETYQESLLFLGVLAAIGLGLNLIFLTVYLVCTCCCRRDHTVQTKQQESCCVTWTAVVAGLLCCAAVGVGFYGNSETNDGMHQLIYSLDNANHTFSGMDELVSANTQRMKVDLEQHLARLSEIIAARGDYIQTLKFMQQMAGNVVSQLSGLPVWREVTTQLTKLSHQTAYVEYYRWLSYLLLFILDLVICLVTCLGLARRSKCLLASMLCCGILTLILSWASLAADAAAAVGTSDFCMAPDIYILNNTGSQINSEVTRYYLHCSQSLISPFQQSLTTFQRSLTTMQIQVGGLLQFAVPLFPTAEKDLLGIQLLLNNSEISLHQLTAMLDCRGLHKDYLDALTGICYDGIEGLLFLGLFSLLAALAFSTLTCAGPRAWKYFINRDRDYDDIDDDDPFNPQARRIAAHNPTRGQLHSFCSYSSGLGSQCSLQPPSQTISNAPVSEYMNQAILFGGNPRYENVPLIGRGSPPPTYSPSMRPTYMSVADEHLRHYEFPSSNSLEVLFQ

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 \(c\).

\(|P_{f(5WJH_1)}(2) \setminus P_{f(3DIQ_1)}(2)|=164\), \(|P_{f(3DIQ_1)}(2) \setminus P_{f(5WJH_1)}(2)|=10\). 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 1:110001111110100001100000000011010010110011010010101010110000000001010100011011000011100001111011000101000011111011100000000101111010111100001001110100011111111100010100001100101001110000000001000101101111100110011110000101001101011111101101100011010001100100101001111010111000001
Pair \(Z_2\) Length of longest common subsequence
5WJH_1,3DIQ_1 174 3
5WJH_1,7RTV_1 174 4
3DIQ_1,7RTV_1 252 3

Newick tree

 
[
	7RTV_1:11.48,
	[
		5WJH_1:87,3DIQ_1:87
	]:27.48
]

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 \((0.85)(0.8)(\frac{453 }{\log_{20} 453}-\frac{174}{\log_{20}174})=82.1\)
Status Protein1 Protein2 d d1/2
Query variables 5WJH_1 3DIQ_1 117 80.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]