CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6CDC_1 8OTO_1 5IFB_1 Letter Amino acid
7 18 26 I Isoleucine
8 18 19 T Threonine
8 19 21 V Valine
7 20 26 A Alanine
5 22 22 N Asparagine
11 9 44 E Glutamic acid
13 12 19 F Phenylalanine
4 7 10 W Tryptophan
14 13 11 Y Tyrosine
5 9 25 R Arginine
12 18 25 D Aspartic acid
13 20 25 G Glycine
3 10 24 P Proline
15 23 36 S Serine
11 33 49 L Leucine
15 18 35 K Lycine
1 12 16 M Methionine
2 5 11 C Cysteine
6 13 12 Q Glutamine
7 5 8 H Histidine 

6CDC_1|Chain A|Glucose-induced degradation protein 4 homolog|Homo sapiens (9606)
>8OTO_1|Chain A|2'-O-methyltransferase nsp16|Severe acute respiratory syndrome coronavirus 2 (2697049)
>5IFB_1|Chain A|Polymerase acidic protein|Influenza A virus (strain A/Wilson-Smith/1933 H1N1) (381518)
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 \(w=f(c)\)
6CDC , Knot 82 167 0.83 40 129 162 
GSGSKFRGHQKSKGNSYDVEVVLQHVDTGNSYLCGYLKIKGLTEEYPTLTTFFEGEIISKKHPFLTRKWDADEDVDRKHWGKFLAFYQYAKSFNSDDFDYEELKNGDYVFMRWKEQFLVPDHTIKDISGASFAGFYYICFQKSAASIEGYYYHRSSEWYQSLNLTHV
8OTO , Knot 137 304 0.86 40 202 294 
SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNNENLYFQ
5IFB , Knot 194 464 0.85 40 246 445 
GNARIEPFLKSTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMRTFFGWKEPNVVKPHEKGINPNYLLSWKQVLAELQDIENEEKIPRTKNMKKTSQLKWALGENMAPEKVDFDDCKDVGDLKQYDSDEPELRSLASWIQNEFNKACELTDSSWIELDEIGEDAAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEVGDMLLRSAIGHVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMTKEFFENKSETWPVGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALR

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 \(c\).

\(|P_{f(6CDC_1)}(2) \setminus P_{f(8OTO_1)}(2)|=63\), \(|P_{f(8OTO_1)}(2) \setminus P_{f(6CDC_1)}(2)|=136\). 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 1:10100101000001000010111001001000101010101100001010011010110000111000101000100001101111000100100001000010010011101000111100010010110111100101000110101000000001000101001
Pair \(Z_2\) Length of longest common subsequence
6CDC_1,8OTO_1 199 3
6CDC_1,5IFB_1 205 3
8OTO_1,5IFB_1 192 3

Newick tree

 
[
	6CDC_1:10.62,
	[
		8OTO_1:96,5IFB_1:96
	]:6.62
]

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 \((0.85)(0.8)(\frac{471 }{\log_{20} 471}-\frac{167}{\log_{20}167})=89.4\)
Status Protein1 Protein2 d d1/2
Query variables 6CDC_1 8OTO_1 119 89.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]