CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8JBB_1 6MQD_1 6DJF_1 Letter Amino acid
5 1 11 M Methionine
17 10 20 Y Tyrosine
29 5 22 V Valine
17 8 21 D Aspartic acid
43 6 22 E Glutamic acid
20 19 37 K Lycine
7 1 19 H Histidine
5 3 21 I Isoleucine
12 5 46 S Serine
72 5 29 A Alanine
0 14 3 C Cysteine
36 10 32 G Glycine
16 2 21 F Phenylalanine
27 5 32 P Proline
11 5 20 T Threonine
39 5 12 R Arginine
14 1 16 Q Glutamine
81 9 46 L Leucine
8 7 16 N Asparagine
5 1 15 W Tryptophan 

8JBB_1|Chains A, B|CRISPR system endoribonuclease Csm6|Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (300852)
>6MQD_1|Chains A, B|Basic phospholipase A2 homolog 2|Bothrops moojeni (98334)
>6DJF_1|Chains A, B|Tyrosyl-DNA phosphodiesterase 1|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 \(w=f(c)\)
8JBB , Knot 175 464 0.77 38 183 394 
MEDLDALWERYREAVRAGGNPQALYQEMVWPALLALWREKPRVYPFPQAFAVSVHTLGTSPEATALAILGAGAERVYVLHTPESARFLPRLRQDTGKDLYPVEIGKSDVEAIYREVKRLLEKHPEVPVALDLTSGTKAMSAGLAAAGFFFQRFYPKVRVVYVDNEDYDPELRRPRAGTEKLRILPNPHEALAEVDALFAKELYGKGEFGQAAAYFRGMVGRTGNQAYALYALLAEMYRAWRALDFGEALKAGRKLLGQLSQNVWLNHPLNARREALEAQVALLEAVDRFLKARDFALKEGVYGLARTLLHLAQEAKEEAAVLAALYAYRALELLLQERLALLGRRAEAPGLSPEEAEALRKALAELLGVLPEEVRLPAKLGLLDLLAFLRLKGDEALGRLSLAELRGLAGALKGRNSALLVHGFDVPSPKAVEGIARLAQGLLQDLEARTALGPLSPEPVPLGF
6MQD , Knot 59 122 0.77 40 92 119 
SLFELGKMILQETGKNPAKSYGVYGCNCGVGGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNSCLKELCECDKAVAICLRENLDTYNKKYRYNYLKPFCKKADPC
6DJF , Knot 195 461 0.86 40 245 439 
SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS

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 \(c\).

\(|P_{f(8JBB_1)}(2) \setminus P_{f(6MQD_1)}(2)|=137\), \(|P_{f(6MQD_1)}(2) \setminus P_{f(8JBB_1)}(2)|=46\). 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 1:10010111000001101110101100011111111110001010111011110100110010101111111110010110010010111010000100101101100010110001001100010111110100100110111111111100101010110100000010100101100010111010011101011110010101011011101011110010010110111101001101101101101100111010001110011010001101011110110011010011100110111001101100100011111110100110111000111110010111101001011001110111111001011101111011111010100111010110101111110100011110110110101101110110111001010011111010111111
Pair \(Z_2\) Length of longest common subsequence
8JBB_1,6MQD_1 183 4
8JBB_1,6DJF_1 156 5
6MQD_1,6DJF_1 225 3

Newick tree

 
[
	6MQD_1:10.50,
	[
		8JBB_1:78,6DJF_1:78
	]:31.50
]

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 \((0.85)(0.8)(\frac{586 }{\log_{20} 586}-\frac{122}{\log_{20}122})=135.\)
Status Protein1 Protein2 d d1/2
Query variables 8JBB_1 6MQD_1 163 103.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]