CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8QLX_1 2ZMK_1 5ADX_1 Letter Amino acid
8 14 24 A Alanine
4 0 2 C Cysteine
9 10 10 Q Glutamine
16 17 28 G Glycine
9 16 28 I Isoleucine
0 4 4 W Tryptophan
12 9 31 E Glutamic acid
5 5 9 H Histidine
3 18 20 F Phenylalanine
8 18 19 P Proline
21 21 27 S Serine
18 8 25 R Arginine
9 12 19 D Aspartic acid
15 15 31 L Leucine
3 9 23 K Lycine
5 0 8 M Methionine
9 21 15 T Threonine
17 22 24 V Valine
4 16 9 N Asparagine
6 6 14 Y Tyrosine 

8QLX_1|Chain A|Putative vacuolar ATPase MVP1|Pyricularia grisea (148305)
>2ZMK_1|Chains A, B, C, D|Basic agglutinin|Psophocarpus tetragonolobus (3891)
>5ADX_1|Chains A, B, C, D, E, F, G, I|ACTIN RELATED PROTEIN 1|SUS SCROFA (9823)
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 \(w=f(c)\)
8QLX , Knot 83 181 0.79 38 128 175 
MGYYEDDRETIEISESRVSRGSSRGPRSRGGDYAPNTVSIPCHHIRLGDILLLQGRPCQVIRISTSAATGQHRYLGVDLFTKELREESSSISTPSPSVVVQTMCGPVFKQYRVLDMQAGHIVAMTETGDVKQNLPVSEQSNLYERLQRAFESGRGSVRALVVSDNGRELVCDMAVLHGSRL
2ZMK , Knot 112 241 0.85 36 166 234 
KTISFNFNQFHQNEEQLKLQRDARISSNSVLELTKVVNGVPTWNSTGRALYAKPVQVWDSTTGNVASFETRFSFSIRQPFPRPHPADGLVFFIAPPNTQTGEGGGYFGIYNPLSPYPFVAVEFDTFRNTWDPQIPHIGIDVNSVISTKTVPFTLDNGGIANVVIKYDASTKILHVVLVFPSLGTIYTIADIVDLKQVLPESVNVGFSAATGDPSGKQRNATETHDILSWSFSASLPGTNEF
5ADX , Knot 158 370 0.84 40 214 355 
IANQPVVIDNGSGVIKAGFAGDQIPKYCFPNYVGRPKHVRVMAGALEGDIFIGPKAEEHRGLLSIRYPMEHGIVKDWNDMERIWQYVYSKEQLQTFSEEHPVLLTEAPLNPRKNRERAAEVFFETFNVPALFISMQAVLSLYATGRTTGVVLDSGDGVTHAVPIYEGFAMPHSIMRIDIAGRDVSRFLRLYLRKEGYDFHSSSEFEIVKAIKERACYLSINPQKDETLETEKAQYYLPDGSTIEIGPSRFRAPELLFRPDLIGEESEGIHEVLVFAIQKSDMDLRRTLFSNIVLSGGSTLFKGFGDRLLSEVKKLAPKDVKIRISAPQERLYSTWIGGSILASLDTFKKMWVSKKEYEEDGARSIHRKTF

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 \(c\).

\(|P_{f(8QLX_1)}(2) \setminus P_{f(2ZMK_1)}(2)|=59\), \(|P_{f(2ZMK_1)}(2) \setminus P_{f(8QLX_1)}(2)|=97\). 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 1:1100000000101000010010001100011001100101100010110111101010011010001101000011101100010000001001010111001011110000110101101111000101000111000001000100110010101011110001001100111101001
Pair \(Z_2\) Length of longest common subsequence
8QLX_1,2ZMK_1 156 5
8QLX_1,5ADX_1 164 4
2ZMK_1,5ADX_1 158 4

Newick tree

 
[
	5ADX_1:81.33,
	[
		8QLX_1:78,2ZMK_1:78
	]:3.33
]

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 \((0.85)(0.8)(\frac{422 }{\log_{20} 422}-\frac{181}{\log_{20}181})=71.2\)
Status Protein1 Protein2 d d1/2
Query variables 8QLX_1 2ZMK_1 90 78.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]