CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3QZZ_1 8XPA_1 6AOI_1 Letter Amino acid
7 0 24 N Asparagine
6 0 8 W Tryptophan
16 0 15 Y Tyrosine
9 0 37 R Arginine
0 2 9 C Cysteine
18 0 39 E Glutamic acid
5 0 17 H Histidine
8 0 27 I Isoleucine
16 0 47 L Leucine
8 0 29 S Serine
14 1 33 T Threonine
13 1 43 A Alanine
10 3 32 G Glycine
9 0 28 F Phenylalanine
12 0 45 V Valine
10 0 34 D Aspartic acid
7 0 18 Q Glutamine
13 0 31 K Lycine
4 0 18 M Methionine
10 0 32 P Proline 

3QZZ_1|Chain A|Methanosarcina acetivorans protoglobin|Methanosarcina acetivorans (2214)
>8XPA_1|Chains A, D, E[auth F], H|DNA (5'-D(P*AP*CP*GP*GP*CP*GP*T)-3')|synthetic construct (32630)
>6AOI_1|Chains A, B|Bifunctional dihydrofolate reductase-thymidylate synthase|Toxoplasma gondii (5811)
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 \(w=f(c)\)
3QZZ , Knot 93 195 0.83 38 149 188 
MSVEKIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWWGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF
8XPA , Knot 5 7 0.46 8 5 5 
ACGGCGT
6AOI , Knot 229 566 0.85 40 274 525 
MQKPVCLVVAMTPKRGIGINNGLPWPHLTTDFKHFSRVTKTTPEEASRFNAVVMGRKTWESMPRKFRPLVDRLNIVVSSSLKEEDIAAEKPQAEGQQRVRVCASLPAALSLLEEEYKDSVDQIFVVGGAGLYEAALSLGVASHLYITRVAREFPCDVFFPAFPGDDILSNKSTAAEKDNEATYRPIFISKTFSDNGVPYDFVVLEKRRKTDDAATAEPSNAMSSLTSTRETTPVHGLQAPSSAAAIAPVLAWMDEEDRKKREQKELIRAVPHVHFRGHEEFQYLDLIADIINNGRTMDDRTGVGVISKFGCTMRYSLDQAFPLLTTKRVFWKGVLEELLWFIRGDTNANHLSEKGVKIWDKNVTREFLDSRNLPHREVGDIGPGYGFQWRHFGAAYKDMHTDYTGQGVDQLKNVIQMLRTNPTDRRMLMTAWNPAALDEMALPPCHLLCQFYVNDQKELSCIMYQRSCDVGLGVPFNIASYSLLTLMVAHVCNLKPKEFIHFMGNTHVYTNHVEALKEQLRREPRPFPIVNILNKERIKEIDDFTAEDFEVVGYVPHGRIQMEMAV

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 \(c\).

\(|P_{f(3QZZ_1)}(2) \setminus P_{f(8XPA_1)}(2)|=148\), \(|P_{f(8XPA_1)}(2) \setminus P_{f(3QZZ_1)}(2)|=4\). 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 1:101001110001000001110100101100111101000001001101100010011001111110010110010010101000011110001001110000000001110000011100000000000010011011000111110110101011110010010010010011101001011110010100101
Pair \(Z_2\) Length of longest common subsequence
3QZZ_1,8XPA_1 152 2
3QZZ_1,6AOI_1 189 5
8XPA_1,6AOI_1 275 2

Newick tree

 
[
	6AOI_1:12.96,
	[
		3QZZ_1:76,8XPA_1:76
	]:52.96
]

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 \((0.85)(0.8)(\frac{202 }{\log_{20} 202}-\frac{7}{\log_{20}7})=70.1\)
Status Protein1 Protein2 d d1/2
Query variables 3QZZ_1 8XPA_1 92 47.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]