CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
9FWP_1 5UYL_1 7AHR_1 Letter Amino acid
3 9 9 H Histidine
6 15 37 L Leucine
5 4 14 F Phenylalanine
7 17 17 P Proline
7 10 23 D Aspartic acid
3 11 20 E Glutamic acid
13 34 18 G Glycine
8 24 9 K Lycine
1 2 5 W Tryptophan
7 15 5 N Asparagine
4 6 8 Q Glutamine
4 11 7 I Isoleucine
3 5 5 M Methionine
6 10 11 S Serine
13 14 17 T Threonine
5 6 6 Y Tyrosine
9 26 26 V Valine
13 21 29 A Alanine
1 29 21 R Arginine
13 2 4 C Cysteine 

9FWP_1|Chain A|Non-structural protein 10|Severe acute respiratory syndrome coronavirus 2 (2697049)
>5UYL_1|Chain A[auth 04]|50S ribosomal protein L2|Escherichia coli (strain K12) (83333)
>7AHR_1|Chains A, B|Chorismate dehydratase|Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (100226)
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 \(w=f(c)\)
9FWP , Knot 66 131 0.81 40 109 128 
AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCD
5UYL , Knot 117 271 0.80 40 171 260 
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS
7AHR , Knot 125 291 0.81 40 175 274 
MVDNSRTRPRVGHIQFLNCLPLYWGLARTGTLLDFELTKDTPEKLSEQLVRGDLDIGPVTLVEFLKNADDLVAFPDIAVGCDGPVMSCVIVSQVPLDRLDGARVALGSTSRTSVRLAQLLLSERFGVQPDYYTCPPDLSLMMQEADAAVLIGDAALRANMIDGPRYGLDVHDLGALWKEWTGLPFVFAVWAARRDYAEREPVITRKVHEAFLASRNLSLEEVEKVAEQAARWEAFDEDTLAKYFTTLDFRFGAPQLEAVTEFARRVGPTTGFPADVKVELLKPLEHHHHHH

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 \(c\).

\(|P_{f(9FWP_1)}(2) \setminus P_{f(5UYL_1)}(2)|=49\), \(|P_{f(5UYL_1)}(2) \setminus P_{f(9FWP_1)}(2)|=111\). 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 1:11010011100011010111101101000011011011000101100001010110101010100001111000100000100101011001010010110001001111010001001011101010000
Pair \(Z_2\) Length of longest common subsequence
9FWP_1,5UYL_1 160 4
9FWP_1,7AHR_1 166 3
5UYL_1,7AHR_1 176 4

Newick tree

 
[
	7AHR_1:87.30,
	[
		9FWP_1:80,5UYL_1:80
	]:7.30
]

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 \((0.85)(0.8)(\frac{402 }{\log_{20} 402}-\frac{131}{\log_{20}131})=81.8\)
Status Protein1 Protein2 d d1/2
Query variables 9FWP_1 5UYL_1 101 74
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]