CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2JND_1 2EWR_1 4UXJ_1 Letter Amino acid
5 16 9 K Lycine
7 4 5 P Proline
2 14 15 V Valine
3 6 9 F Phenylalanine
6 9 8 S Serine
9 7 6 Y Tyrosine
7 4 16 A Alanine
7 4 3 N Asparagine
2 4 8 M Methionine
5 3 10 Q Glutamine
9 11 10 G Glycine
2 3 1 W Tryptophan
8 19 12 E Glutamic acid
4 9 10 H Histidine
4 14 9 I Isoleucine
8 14 12 L Leucine
12 6 10 T Threonine
7 12 16 R Arginine
6 10 13 D Aspartic acid
6 1 9 C Cysteine 

2JND_1|Chain A|Corticotropin-releasing factor receptor 2|Mus musculus (10090)
>2EWR_1|Chain A|hypothetical protein TM1012|Thermotoga maritima (2336)
>4UXJ_1|Chains A, B, C, D, E, F, G, H|THYMIDINE KINASE|LEISHMANIA MAJOR (5664)
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 \(w=f(c)\)
2JND , Knot 60 119 0.80 40 101 115 
GSGMKETAAAKFERQHMDSPDLGTTLLEQYCHRTTIGNFSGPYTYCNTTLDQIGTCWPQSAPGALVERPCPEYFNGIKYNTTRNAYRECLENGTWASRVNYSHCEPILDDKQRKYDLHY
2EWR , Knot 81 170 0.81 40 119 164 
MGSDKIHHHHHHMIRPEYLRVLRKIYDRLKNEKVNWVVTGSLSFALQGVPVEVHDIDIQTDEEGAYEIERIFSEFVSKKVRFSSTEKICSHFGELIIDGIKVEIMGDIRKRLEDGTWEDPVDLNKYKRFVETHGMKIPVLSLEYEYQAYLKLGRVEKAETLRKWLNERKG
4UXJ , Knot 92 191 0.84 40 150 183 
MSGHHHHHHFRGRIELIIGPMFAGKTTELMRRVKREIHARRSCFVIKYSKDTRYDEHNVASHDQLMLRAQAAVSQLTEVRDTWKRFDVLAIDEGQFFSDLVDFCNTAADAGKVVMVSALDGDYRRKPFGQICELVPYCEAVDKLTAVCMMCHEQPACFTRRTVNVEQQELIGGADMYIATCRECYSKQQLP

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 \(c\).

\(|P_{f(2JND_1)}(2) \setminus P_{f(2EWR_1)}(2)|=72\), \(|P_{f(2EWR_1)}(2) \setminus P_{f(2JND_1)}(2)|=90\). 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 1:10110001110100001001011001100000000110101100000001001100110011111100101001011000000010000100101100100000011100000000100
Pair \(Z_2\) Length of longest common subsequence
2JND_1,2EWR_1 162 3
2JND_1,4UXJ_1 169 3
2EWR_1,4UXJ_1 169 6

Newick tree

 
[
	4UXJ_1:85.63,
	[
		2JND_1:81,2EWR_1:81
	]:4.63
]

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 \((0.85)(0.8)(\frac{289 }{\log_{20} 289}-\frac{119}{\log_{20}119})=53.1\)
Status Protein1 Protein2 d d1/2
Query variables 2JND_1 2EWR_1 66 57
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]