CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
9CHM_1 6ACN_1 7SSP_1 Letter Amino acid
8 57 8 I Isoleucine
10 44 19 T Threonine
5 20 6 Y Tyrosine
9 22 9 F Phenylalanine
11 36 25 S Serine
13 42 15 V Valine
12 59 34 A Alanine
2 12 3 C Cysteine
9 72 19 G Glycine
3 25 10 H Histidine
7 36 22 R Arginine
5 47 15 D Aspartic acid
32 63 35 L Leucine
17 53 9 K Lycine
6 43 14 P Proline
2 9 6 W Tryptophan
5 34 10 N Asparagine
11 28 22 Q Glutamine
15 42 25 E Glutamic acid
2 10 12 M Methionine 

9CHM_1|Chain A[auth E]|Fanconi-associated nuclease 1|Homo sapiens (9606)
>6ACN_1|Chain A|ACONITASE|Sus scrofa (9823)
>7SSP_1|Chains A, B, C, D|Ubiquinone biosynthesis protein COQ9, mitochondrial|Homo sapiens (9606)
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 \(w=f(c)\)
9CHM , Knot 85 184 0.80 40 126 177 
HPYYLRSFLVVLKTVLENEDDMLLFDEQEKGIVTKFYQLSATGQKLYVRLFQRKLSWIKMTKLEYEEIALDLTPVIEELTNAGFLQTESELQELSEVLELLSAPELKSLAKTFHLVNPNGQKQQLVDAFLKLAKQHSVCTWGKNKPGIGAVILKRAKALAGQSVRICKGPRAVFSRILLLFSLT
6ACN , Knot 293 754 0.85 40 291 679 
QRAKVAMSHFEPHEYIRYDLLEKNIDIVRKRLNRPLTLSEKIVYGHLDDPANQEIERGKTYLRLRPDRVAMQDATAQMAMLQFISSGLPKVAVPSTIHCDHLIEAQLGGEKDLRRAKDINQEVYNFLATAGAKYGVGFWRPGSGIIHQIILENYAYPGVLLIGTDSHTPNGGGLGGICIGVGGADAVDVMAGIPWELKCPKVIGVKLTGSLSGWTSPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGMATICNMGAEIGATTSVFPYNHRMKKYLSKTGRADIANLADEFKDHLVPDPGCHYDQVIEINLSELKPHINGPFTPDLAHPVAEVGSVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTITPGSEQIRATIERDGYAQVLRDVGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDANPETHAFVTSPEIVTALAIAGTLKFNPETDFLTGKDGKKFKLEAPDADELPRAEFDPGQDTYQHPPKDSSGQRVDVSPTSQRLQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAAGPWLKFRGHLDNISNNLLIGAINIENRKANSVRNAVTQEFGPVPDTARYYKQHGIRWVVIGDENYGEGSSREHSALEPRHLGGRAIITKSFARIHETNLKKQGLLPLTFADPADYNKIHPVDKLTIQGLKDFAPGKPLKCIIKHPNGTQETILLNHTFNETQIEWFRAGSALNRMKELQQK
7SSP , Knot 137 318 0.82 40 193 303 
MAAAAVSGALGRAGWRLLQLRCLPVARCRQALVPRAFHASAVGLRSSDEQKQQPPNSFSQQHSETQGAEKPDPESSHSPPRYTDQGGEEEEDYESEEQLQHRILTAALEFVPAHGWTAEAIAEGAQSLGLSSAAASMFGKDGSELILHFVTQCNTRLTRVLEEEQKLVQLGQAEKRKTDQFLRDAVETRLRMLIPYIEHWPRALSILMLPHNIPSSLSLLTSMVDDMWHYAGDQSTDFNWYTRRAMLAAIYNTTELVMMQDSSPDFEDTWRFLENRVNDAMNMGHTAKQVKSTGEALVQGLMGAAVTLKNLTGLNQRR

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 \(c\).

\(|P_{f(9CHM_1)}(2) \setminus P_{f(6ACN_1)}(2)|=20\), \(|P_{f(6ACN_1)}(2) \setminus P_{f(9CHM_1)}(2)|=185\). 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 1:0100100111110011000001111000001110010010101001010110001011010010000111010111001001111000001001001101101101001100101101010000110111011000010011000111111110010111100101001101110011111010
Pair \(Z_2\) Length of longest common subsequence
9CHM_1,6ACN_1 205 4
9CHM_1,7SSP_1 177 4
6ACN_1,7SSP_1 166 4

Newick tree

 
[
	9CHM_1:99.64,
	[
		7SSP_1:83,6ACN_1:83
	]:16.64
]

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 \((0.85)(0.8)(\frac{938 }{\log_{20} 938}-\frac{184}{\log_{20}184})=207.\)
Status Protein1 Protein2 d d1/2
Query variables 9CHM_1 6ACN_1 264 161.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]