CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2VWM_1 2ICJ_1 8BQE_1 Letter Amino acid
7 18 60 N Asparagine
9 6 0 C Cysteine
23 10 124 G Glycine
5 8 3 H Histidine
19 19 11 K Lycine
4 4 2 W Tryptophan
14 9 8 R Arginine
11 10 53 D Aspartic acid
9 8 20 Q Glutamine
12 9 31 F Phenylalanine
11 10 75 S Serine
20 10 190 T Threonine
20 23 9 E Glutamic acid
14 28 76 L Leucine
14 14 203 A Alanine
13 18 40 I Isoleucine
5 4 4 M Methionine
7 11 8 P Proline
8 6 15 Y Tyrosine
16 8 94 V Valine 

2VWM_1|Chains A, B|ACTIVATED FACTOR XA HEAVY CHAIN|HOMO SAPIENS (9606)
>2ICJ_1|Chain A|Isopentenyl-diphosphate delta isomerase|Homo sapiens (9606)
>8BQE_1|Chains A, B, C, D, E, F|S-layer protein rsaA|Caulobacter vibrioides NA1000 (565050)
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 \(w=f(c)\)
2VWM , Knot 111 241 0.84 40 174 233 
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGEQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLPKAK
2ICJ , Knot 105 233 0.81 40 158 222 
GPLGSMMPEINTNHLDKQQVQLLAEMCILIDENDNKIGAETKKNCHLNENIEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNPAELEESDALGVRRAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSKEELKELLKKAASGEIKITPWFKIIAATFLFKWWDNLNHLNQFVDHEKIYRM
8BQE , Knot 316 1026 0.71 38 191 620 
MAYTTAQLVTAYTNANLGKAPDAATTLTLDAYATQTQTGGLSDAAALTNTLKLVNSTTAVAIQTYQFFTGVAPSAAGLDFLVDSTTNTNDLNDAYYSKFAQENRFINFSINLATGAGAGATAFAAAYTGVSYAQTVATAYDKIIGNAVATAAGVDVAAAVAFLSRQANIDYLTAFVRANTPFTAAADIDLAVKAALIGTILNAATVSGIGGYATATAAMINDLSDGALSTDNAAGVNLFTAYPSSGVSGSTLSLTTGTDTLTGTANNDTFVAGEVAGAATLTVGDTLSGGAGTDVLNWVQAAAVTALPTGVTISGIETMNVTSGAAITLNTSSGVTGLTALNTNTSGAAQTVTAGAGQNLTATTAAQAANNVAVDGGANVTVASTGVTSGTTTVGANSAASGTVSVSVANSSTTTTGAIAVTGGTAVTVAQTAGNAVNTTLTQADVTVTGNSSTTAVTVTQTAAATAGATVAGRVNGAVTITDSAAASATTAGKIATVTLGSFGAATIDSSALTTVNLSGTGTSLGIGRGALTATPTANTLTLNVNGLTTTGAITDSEAAADDGFTTINIAGSTASSTIASLVAADATTLNISGDARVTITSHTAAALTGITVTNSVGATLGAELATGLVFTGGAGADSILLGATTKAIVMGAGDDTVTVSSATLGAGGSVNGGDGTDVLVANVNGSSFSADPAFGGFETLRVAGAAAQGSHNANGFTALQLGATAGATTFTNVAVNVGLTVLAAPTGTTTVTLANATGTSDVFNLTLSSSAALAAGTVALAGVETVNIAATDTNTTAHVDTLTLQATSAKSIVVTGNAGLNLTNTGNTAVTSFDASAVTGTGSAVTFVSANTTVGEVVTIRGGAGADSLTGSATANDTIIGGAGADTLVYTGGTDTFTGGTGADIFDINAIGTSTAFVTITDAAVGDKLDLVGISTNGAIADGAFGAAVTLGAAATLAQYLDAAAAGDGSGTSVAKWFQFGGDTYVVVDSSAGATFVSGADAVIKLTGLVTLTTSAFATEVLTLA

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 \(c\).

\(|P_{f(2VWM_1)}(2) \setminus P_{f(2ICJ_1)}(2)|=104\), \(|P_{f(2ICJ_1)}(2) \setminus P_{f(2VWM_1)}(2)|=88\). 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 1:1111000001001101111000001101101100101101100100100101011000000001101100101110000100000010111101001101010111101100011000110000111011100000100000101101101000000100011100011011000000010010011101001000011011101101010010011000101110110001000111010
Pair \(Z_2\) Length of longest common subsequence
2VWM_1,2ICJ_1 192 3
2VWM_1,8BQE_1 167 4
2ICJ_1,8BQE_1 177 4

Newick tree

 
[
	2ICJ_1:95.08,
	[
		2VWM_1:83.5,8BQE_1:83.5
	]:11.58
]

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 \((0.85)(0.8)(\frac{474 }{\log_{20} 474}-\frac{233}{\log_{20}233})=69.6\)
Status Protein1 Protein2 d d1/2
Query variables 2VWM_1 2ICJ_1 94 91
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]