CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4YDU_1 8HNU_1 1IAW_1 Letter Amino acid
6 67 0 N Asparagine
8 34 0 Q Glutamine
12 23 0 H Histidine
11 22 0 M Methionine
24 60 0 V Valine
45 71 1 A Alanine
16 62 0 E Glutamic acid
14 61 0 F Phenylalanine
24 61 0 D Aspartic acid
34 63 7 G Glycine
13 61 0 I Isoleucine
36 87 0 L Leucine
20 63 2 T Threonine
2 8 0 W Tryptophan
20 37 0 R Arginine
3 0 7 C Cysteine
16 72 0 K Lycine
18 33 0 P Proline
13 59 0 S Serine
8 49 0 Y Tyrosine 

4YDU_1|Chains A, B|tRNA N6-adenosine threonylcarbamoyltransferase|Escherichia coli (562)
>8HNU_1|Chains A, B|Cellodextrin phosphorylase|Acetivibrio thermocellus (1515)
>1IAW_1|Chains A[auth C], B[auth D], C[auth E], D[auth F]|5'-D(*TP*GP*CP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*GP*GP*C)-3'|
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 \(w=f(c)\)
4YDU , Knot 147 343 0.83 40 192 317 
MRVLGIETSCDETGIAIYDDEKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKESGLTAKDIDAVAYTAGPGLVGALLVGATVGRSLAFAWDVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPLLSKMAAQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRDNGTDDQTRADIARAFEDAVVDTLMIKCKRALDQTGFKRLVMAGGVSANRTLRAKLAEMMKKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGATADLGVSVRPRWPLAELPAAHHHHHH
8HNU , Knot 369 993 0.85 38 304 893 
MGITKVTARNNKITPVELLNQKFGNKINLGNFADAVFTDAAFKNVAGIANLPMKAPVMQVLMENSIVSKYLKQFVPDRSVSFVEEGQKFYIVLEDGQKIEVPEDVNKALKATVSDVKHWAGYLTEDGEHVIDLLKPAPGPHFYVNLLIGNRLGFKRTLQTTPKSVVDRFGRGSFRSHAATQVLATRFDMRQEENGFPANRQFYLYEDGKQIFYSALIDDNIVEATSKHSSNRTVIKYKTASNLEITRTIFLVPHKKGFPLATELQRIEIKNASDKARNLSITYTGMFGTGAVHAIFEDVTYTNVIMQSAALYNDKGEFIGITPDYYPEEFKQDTRFVTMIVRNGDEKSFPQSFSTDYNDFVGTGTLEHPAGGSNLNNKLNRKGPGFFALGAPFTVEPGKTVIIDTFTGLSSSKDNENYSDAVMLRELDNLLRYFEKSESVEETLNEIINFHENYGKYFQFNTGNKLFDSGFNRNLAFQVLYQTFMSRSFGQTQKGYREIGFREIQDLFASMYYFINIGYQDFVKELLFEWTANVYKMGYANHNFYWVGKQPGLYSDDSLWLLQAYYRYIIYTKDTSVLNEEVPVADGNNEKRAVRETLKAIIQYSASISVGDHGLPLLDLADWNDSLKIDSNSIDGATKEKLYYEQLKKTNGKYGDRFMSDYSESVMNAFLLKLAIDHLAEIATLDNDTQLAQQMSELSKEVTDRIQKHAWKENFFARVLINRYKDGSYTYLGAKGDKLSADPNIDGVYFLNSFAWSVLSDVATDEQIAIMVDVIKKHLLTPYGLRLVTPADLNKIANDTATGHYFFGDRENGAVFKHASMMAVAALIKAAKKVKDNELAKEMARIAYFMIDLVLPYKNLENPFQVAGNPRISTQYINTDTGENIGPLLSGTATWLNLNLISLAGIEYTRDGISFNPILREEETQLNFTLKAPKSSYKFSITKPVGFARMESSEYELFVDGQKIDNTVIPMYTDEKEHIVTLKFKLEHHHHHH
1IAW , Knot 9 17 0.50 8 8 13 
TGCCACGCCGGCGTGGC

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 \(c\).

\(|P_{f(4YDU_1)}(2) \setminus P_{f(8HNU_1)}(2)|=24\), \(|P_{f(8HNU_1)}(2) \setminus P_{f(4YDU_1)}(2)|=136\). 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 1:1011110000000111100000111100100010101001111101100001000111101110001101001011100111111111111101100111110111111001010111111000110111111110110001101011100011100100111011000101111001111110011101011011110110001110101011001110010001000000101101100111001110000110001100111111101000101011011000010110101010000111110111101011101011101010111101111000000
Pair \(Z_2\) Length of longest common subsequence
4YDU_1,8HNU_1 160 6
4YDU_1,1IAW_1 194 2
8HNU_1,1IAW_1 306 3

Newick tree

 
[
	1IAW_1:14.51,
	[
		4YDU_1:80,8HNU_1:80
	]:60.51
]

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 \((0.85)(0.8)(\frac{1336 }{\log_{20} 1336}-\frac{343}{\log_{20}343})=258.\)
Status Protein1 Protein2 d d1/2
Query variables 4YDU_1 8HNU_1 331 219
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]