CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6WMP_1 9GOI_1 1DTX_1 Letter Amino acid
23 13 3 E Glutamic acid
19 49 5 G Glycine
28 14 4 I Isoleucine
11 2 3 F Phenylalanine
28 30 2 S Serine
0 6 1 W Tryptophan
17 47 1 A Alanine
24 17 4 N Asparagine
2 4 6 C Cysteine
10 9 3 Q Glutamine
23 7 6 K Lycine
10 20 3 P Proline
33 33 0 V Valine
11 10 8 R Arginine
38 19 2 L Leucine
15 26 2 T Threonine
5 15 3 Y Tyrosine
21 22 2 D Aspartic acid
2 7 1 H Histidine
3 6 0 M Methionine 

6WMP_1|Chain A|DNA-directed RNA polymerase subunit alpha 1|Francisella tularensis subsp. holarctica (strain LVS) (376619)
>9GOI_1|Chain A|Alkaline serine protease|Stenotrophomonas maltophilia (40324)
>1DTX_1|Chain A|ALPHA-DENDROTOXIN|Dendroaspis angusticeps (8618)
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 \(w=f(c)\)
6WMP , Knot 138 323 0.82 38 174 310 
MSNNNSKLEFVPNIQLKEDLGAFSYKVQLSPVEKGMAHILGNSIRRVLLSSLSGASIIKVNIANVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDTGIDRLDLELSVNKSGVVSAGDFKTTQGVEIINKDQPIATLTNQRAFSLTATVSVGRNVGILSAIPTELERVGDIAVDADFNPIKRVAFEVFDNGDSETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVPSNGKTGDVLIDSNIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQILIDNNLSLGVQIDNFRELVEGK
9GOI , Knot 150 356 0.82 40 188 325 
LAPNDPYYQEYQWHLHNATGGINAPSAWDVSQGEGVVVAVLDTGILPQHPDLVGNLLEGYDFISDASTSRRATNDRVPGAQDYGDWVENDNECYTGSVAEDSSWHGTHVAGTVAEQTNNGVGMAGVAHKAKVLPVRVLGKCGGYLSDIADAITWASGGTVAGVPANANPAEVINMSLGGSGSCDGTYQDAINGAISRGTTVVVAAGNETDNASKYRPASCDGVVTVGATRITGGITYYSNYGSRVDLSGPGGGGSVDGNPGGYVWQSGSDAATTPESGSYSYMGMGGTSMASPHVAAVAALVQSALIASGKDPLAPAAMRTLLKETARPFPVSIPTATPIGTGIVDAKAALAEALE
1DTX , Knot 34 59 0.78 36 54 57 
QPRRKLCILHRNPGRCYDKIPAFYYNQKKKQCERFDWSGCGGNSNRFKTIEECRRTCIG

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 \(c\).

\(|P_{f(6WMP_1)}(2) \setminus P_{f(9GOI_1)}(2)|=68\), \(|P_{f(9GOI_1)}(2) \setminus P_{f(6WMP_1)}(2)|=82\). 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 1:10000001011101010001111000101011001110111001001110010110110101101100000100100011011001001110100110010101010001110110100001101100001110100001101010101100111101110010011011101010110011101100100001011100010101111100110010001011101011001001011100010111101100101010000010100100110110000001101101100010010011100010111010010011010
Pair \(Z_2\) Length of longest common subsequence
6WMP_1,9GOI_1 150 5
6WMP_1,1DTX_1 178 3
9GOI_1,1DTX_1 204 3

Newick tree

 
[
	1DTX_1:10.69,
	[
		6WMP_1:75,9GOI_1:75
	]:26.69
]

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 \((0.85)(0.8)(\frac{679 }{\log_{20} 679}-\frac{323}{\log_{20}323})=98.2\)
Status Protein1 Protein2 d d1/2
Query variables 6WMP_1 9GOI_1 124 118.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]