CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6RGK_1 9FGD_1 5VCL_1 Letter Amino acid
32 29 13 A Alanine
11 10 14 Q Glutamine
16 19 4 I Isoleucine
17 33 10 K Lycine
18 45 17 T Threonine
8 21 14 Y Tyrosine
23 28 18 D Aspartic acid
17 22 19 G Glycine
3 9 10 W Tryptophan
21 25 20 R Arginine
11 13 8 M Methionine
30 35 15 V Valine
10 29 17 P Proline
24 29 17 S Serine
14 17 9 N Asparagine
8 4 5 C Cysteine
28 21 24 E Glutamic acid
11 8 11 H Histidine
37 43 24 L Leucine
21 24 9 F Phenylalanine 

6RGK_1|Chains A, B|Phosphodiesterase|Trypanosoma brucei (5691)
>9FGD_1|Chains A, D|Gamma-aminobutyric acid receptor subunit alpha-1|Homo sapiens (9606)
>5VCL_1|Chain A|H2-T23 protein|Mus musculus (10090)
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 \(w=f(c)\)
6RGK , Knot 152 360 0.82 40 210 350 
GSHMASELNEHRATLFNKNVPSRAVKRVTAITKVEREAVLVCELPSFDVTDVEFDLFRARESTDKPLDVAAAIAYRLLLGSGLPQKFGCSDEVLLNFILQCRKKYRNVPYHNFYHVVDVCQTIHTFLYRGNVYEKLTELECFVLLITALVHDLDHMGLNNSFYLKTESPLGILSSASGNTSVLEVHHCNLAVEILSDPESDVFDGLEGAERTLAFRSMIDCVLATDMAKHGSALEAFLASAADQSSDEAAFHRMTMEIILKAGDISNVTKPFDISRQWAMAVTEEFYRQGDMEKERGVEVLPMFDRSKNMELAKGQIGFIDFVAAPFFQKIVDACLQGMQWTVDRIKSNRAQWERVLETR
9FGD , Knot 188 464 0.83 40 240 435 
MKKSPGLSDYLWAWTLFLSTLTGRSYGDYKDDDDKQPSLQDELKDNTTVFTRILDRLLDGYDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLRITEDGTLLYTMRLTVRAECPMHLEDFPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVILSQVSFWLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVPEKPKKVKDPLIKKNNTYAPTATSYTPNLARGDPGLATIAKSATIEPKEVKPETKPPEPKKTFNSVSKIDRLSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQ
5VCL , Knot 125 278 0.84 40 185 274 
MSSHSLRYFHTAMSRPGLGEPRFIVVGYVDDTQFVSFDSDSENPKMEPRARWMEQEGPEYWERETWKARDMGRNFRVNLRTLLGYYNQSKDESHTLQWMYGCDVGPDGRLLRGYCQEAYDGQDYISLNEDLRSWTATDFASQISKHKSEMVDEAHQQRAYLQGPCVEWLHTYLRLGNKTLKRSDPPKAHVTHHPRSEDYVTLRCWALGFYPADITLTWQLNGEELTQDMEFVETRPAGDGNFQKWASVVVPLGKEQNYTCHVEHEGLPEPLTLRWEPP

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 \(c\).

\(|P_{f(6RGK_1)}(2) \setminus P_{f(9FGD_1)}(2)|=63\), \(|P_{f(9FGD_1)}(2) \setminus P_{f(6RGK_1)}(2)|=93\). 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 1:100110010000101100011001100101100100011110011010100101011010000001101111110011110111001100001110111000000001100010011010001001100101000100100111110111001001110001010000111110010100011010000111011001000110110110001110011001110011001011011110110000001110010101110110100100110100011111000100010100001101111100000101101011110111111100110101011010100100001010011000
Pair \(Z_2\) Length of longest common subsequence
6RGK_1,9FGD_1 156 3
6RGK_1,5VCL_1 193 3
9FGD_1,5VCL_1 191 6

Newick tree

 
[
	5VCL_1:10.29,
	[
		6RGK_1:78,9FGD_1:78
	]:23.29
]

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 \((0.85)(0.8)(\frac{824 }{\log_{20} 824}-\frac{360}{\log_{20}360})=125.\)
Status Protein1 Protein2 d d1/2
Query variables 6RGK_1 9FGD_1 160 142
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]