CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8FCG_1 8CKO_1 8RKX_1 Letter Amino acid
20 23 11 Y Tyrosine
21 33 14 K Lycine
27 33 16 P Proline
32 27 23 T Threonine
10 19 8 M Methionine
15 26 14 F Phenylalanine
15 14 16 Q Glutamine
13 10 3 H Histidine
23 31 28 L Leucine
20 26 10 I Isoleucine
48 38 22 V Valine
43 41 30 A Alanine
12 26 14 R Arginine
17 1 2 C Cysteine
27 30 21 G Glycine
38 20 14 S Serine
4 12 5 W Tryptophan
15 28 17 N Asparagine
18 26 20 D Aspartic acid
21 35 14 E Glutamic acid 

8FCG_1|Chains A, B, C, D|E1 glycoprotein|Chikungunya virus (37124)
>8CKO_1|Chain A|ABC transporter substrate-binding protein|Agrobacterium fabrum str. C58 (176299)
>8RKX_1|Chains A[auth L], B[auth Q], C[auth V], D[auth a], E[auth f], F[auth k], G[auth p]|Bacteriophage Mu GpT domain-containing protein|Pseudomonas phage JBD30 (1223260)
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 \(w=f(c)\)
8FCG , Knot 180 439 0.83 40 243 411 
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDTENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNVTVSAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESEDVYANTQLVLQRPSAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISVTAMSWVQKITGGVGLVVAVAALILIVVLCVSFSRH
8CKO , Knot 206 499 0.85 40 249 465 
MQERRALRLGVNGLPNSLEPVNAISNVGPRIVNQIFDTLIARDFFAKGAPGNAIDLVPALAESWERIDEKSVRFKLRQKVMFHDGVELTADDVAYTFSSERLWGPEAIKKIPLGKSYSLDFDEPVVEDKYTVTLRTKTPSYLIETFVASWMSRIVPKEYYKKLGAVDFGNKPVGTGPYKFVEFVAGDRVVLEANDAYWGPKPTASKITYQIVAEPATRVAGLISGEYDIITTLTPDDIQLINSYPDLETRGTLIENFHMFTFNMNQEVFKDKKLRRALALAVNRPIMVEALWKKQASIPAGFNFPNYGETFDPKRKAMEYNVEEAKRLVKESGYDGTPITYHTMGNYYANAMPALMMMIEMWKQIGVNVVMKTYAPGSFPPDNQTWMRNWSNGQWMTDAYATIVPEFGPNGQVQKRWGWKAPAEFNELCQKVTVLPNGKERFDAYNRMRDIFEEEAPAVILYQPYDVYAARKDVHWKPVSFEMMEFRNNLSFGHHHHHH
8RKX , Knot 126 302 0.79 40 180 294 
IITPALISALKTSFQKHFQDALATAPSTYLQVATVIPSTTASNTYGWLGQFPKLREWIGQRVIKDMAAQGYQITNKLFESTVGVKRTDIEDDNLGVYGPLMQEMGRAAGAHPDELVFALLKAGNANLCYDGQNFFDTDHPVYPNVDGTGTATTVSNLFAPAADPGAAWYLLDTSRSLKPLIYQERMKPSFTSMTKEDDEQVFMADEYRYGVRSRCNVGFGFWQLAAMSTEELNQVNFEKVYDAMRNQKADGGRPLDIRPNLLVVPTTLRSKAKEVVGVQRLANGADNPNFELVQVLDTAWLN

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 \(c\).

\(|P_{f(8FCG_1)}(2) \setminus P_{f(8CKO_1)}(2)|=75\), \(|P_{f(8CKO_1)}(2) \setminus P_{f(8FCG_1)}(2)|=81\). 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 1:0001011100111100011001100111101011010101010100100000011101010001010000001100000110110111111100100000001001010000000001101001001010101011001001010101010011010010111111001101100011100101001001111110110110100001000010100011100101101011000110110011000110100011110011001101100111011101011011100110110100100011100000011111110011000100110010011010010101010001010100111010101010000100110001100011001100001110010101101100101111111111111111110101000
Pair \(Z_2\) Length of longest common subsequence
8FCG_1,8CKO_1 156 4
8FCG_1,8RKX_1 171 5
8CKO_1,8RKX_1 163 3

Newick tree

 
[
	8RKX_1:85.28,
	[
		8FCG_1:78,8CKO_1:78
	]:7.28
]

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 \((0.85)(0.8)(\frac{938 }{\log_{20} 938}-\frac{439}{\log_{20}439})=132.\)
Status Protein1 Protein2 d d1/2
Query variables 8FCG_1 8CKO_1 166 157.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]