CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2XGL_1 5NED_1 3QGC_1 Letter Amino acid
6 13 21 R Arginine
9 8 27 D Aspartic acid
2 4 17 F Phenylalanine
4 6 32 S Serine
7 10 12 Y Tyrosine
6 17 28 V Valine
3 10 20 N Asparagine
7 8 11 H Histidine
6 20 46 L Leucine
5 26 20 T Threonine
2 1 3 W Tryptophan
2 2 13 C Cysteine
4 9 24 Q Glutamine
3 5 26 I Isoleucine
4 2 14 M Methionine
4 14 8 P Proline
4 25 26 A Alanine
11 10 22 E Glutamic acid
6 10 17 G Glycine
8 11 26 K Lycine 

2XGL_1|Chains A, B|COLICIN-M IMMUNITY PROTEIN|Escherichia coli (562)
>5NED_1|Chain A|O PanAsia VP1|Foot-and-mouth disease virus (12110)
>3QGC_1|Chain A|Fem-3 mRNA-binding factor 2|Caenorhabditis elegans (6239)
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 \(w=f(c)\)
2XGL , Knot 55 103 0.82 40 83 98 
MSEDKGPACYQVSDEQARTFVKNDYLQRMKRWDNDVQLLGTEIPKITWEKIERSLTDVEDEKTLLVPFKAEGPDGKRMYYGMYHCEEGYVEYANDRSHHHHHH
5NED , Knot 96 211 0.81 40 139 203 
TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHTLVGALLRTATYYFADLEVAVKHEGNLTWVPNGAPETALDNTTNPTAYHKAPLTRLALPYTAPHRVLATAYNGNCKYGESHTTNVRGDLQVLAQKAARTLPTSFNYGAIKATRVTELLYRMKRAETYCPRPLLAIHPSEARHKQKIVAPVKQ
3QGC , Knot 172 413 0.83 40 230 384 
GSNNVLPTWSLDSNGEMRSRLSLSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACYVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTICCDAVSGRRQTKEGGYDHAISFQDWLKKLHSRVTKERHRLSRFSSGKKMIETLANLRSTHPIYELQ

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 \(c\).

\(|P_{f(2XGL_1)}(2) \setminus P_{f(5NED_1)}(2)|=48\), \(|P_{f(5NED_1)}(2) \setminus P_{f(2XGL_1)}(2)|=104\). 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 1:1000011100010000100110000100100100010111001101010010001001000001111101011010010011000001010010000000000
Pair \(Z_2\) Length of longest common subsequence
2XGL_1,5NED_1 152 4
2XGL_1,3QGC_1 207 4
5NED_1,3QGC_1 197 3

Newick tree

 
[
	3QGC_1:10.09,
	[
		2XGL_1:76,5NED_1:76
	]:32.09
]

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 \((0.85)(0.8)(\frac{314 }{\log_{20} 314}-\frac{103}{\log_{20}103})=65.9\)
Status Protein1 Protein2 d d1/2
Query variables 2XGL_1 5NED_1 83 60.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]