CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5UYM_1 5URN_1 8RSE_1 Letter Amino acid
34 5 38 G Glycine
11 9 16 I Isoleucine
24 11 14 K Lycine
17 5 14 P Proline
10 11 43 S Serine
2 1 2 W Tryptophan
26 9 30 V Valine
21 7 48 A Alanine
15 6 21 N Asparagine
6 4 9 Q Glutamine
11 7 14 E Glutamic acid
5 5 9 M Methionine
4 3 9 F Phenylalanine
14 7 24 T Threonine
29 6 17 R Arginine
2 0 5 C Cysteine
9 3 6 H Histidine
15 6 26 L Leucine
6 1 20 Y Tyrosine
10 9 19 D Aspartic acid 

5UYM_1|Chain A[auth 04]|50S ribosomal protein L2|Escherichia coli (strain K12) (83333)
>5URN_1|Chain A|RNA polymerase II transcription factor B subunit 1|Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (559292)
>8RSE_1|Chain A|Proteinase K|Parengyodontium album (37998)
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 \(w=f(c)\)
5UYM , Knot 117 271 0.80 40 171 260 
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS
5URN , Knot 58 115 0.79 38 96 113 
PSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDAD
8RSE , Knot 159 384 0.82 40 209 364 
MRLSVLLSLLPLALGAPAVEQRSEAAPLIEARGEMVANKYIVKFKEGSALSALDAAMEKISGKPDHVYKNVFSGFAATLDENMVRVLRAHPDVEYIEQDAVVTINAAQTNAPWGLARISSTSPGTSTYYYDESAGQGSCVYVIDTGIEASHPEFEGRAQMVKTYYYSSRDGNGHGTHCAGTVGSRTYGVAKKTQLFGVKVLDDNGSGQYSTIIAGMDFVASDKNNRNCPKGVVASLSLGGGYSSSVNSAAARLQSSGVMVAVAAGNNNADARNYSPASEPSVCTVGASDRYDRRSSFSNYGSVLDIFGPGTDILSTWIGGSTRSISGTSMATPHVAGLAAYLMTLGKTTAASACRYIADTANKGDLSNIPFGTVNLLAYNNYQA

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 \(c\).

\(|P_{f(5UYM_1)}(2) \setminus P_{f(5URN_1)}(2)|=116\), \(|P_{f(5URN_1)}(2) \setminus P_{f(5UYM_1)}(2)|=41\). 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 1:1110001001100011011010100101111110000001100001010000111100010011010000011111100100010001011111000100001111011011001001101110110011100111100100101011011011001100101110011010101001010010100010110110100110111011110101101010101101100101110100110011011110001000000000001110000
Pair \(Z_2\) Length of longest common subsequence
5UYM_1,5URN_1 157 3
5UYM_1,8RSE_1 142 4
5URN_1,8RSE_1 173 3

Newick tree

 
[
	5URN_1:86.11,
	[
		5UYM_1:71,8RSE_1:71
	]:15.11
]

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 \((0.85)(0.8)(\frac{386 }{\log_{20} 386}-\frac{115}{\log_{20}115})=82.6\)
Status Protein1 Protein2 d d1/2
Query variables 5UYM_1 5URN_1 103 72.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]