CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4ESE_1 7FCJ_1 4AFB_1 Letter Amino acid
10 8 7 E Glutamic acid
10 7 15 P Proline
14 6 21 T Threonine
8 7 8 R Arginine
10 14 27 S Serine
6 9 13 N Asparagine
0 2 6 C Cysteine
12 13 2 Q Glutamine
2 11 13 H Histidine
14 13 8 I Isoleucine
8 9 14 K Lycine
1 4 2 W Tryptophan
28 5 15 A Alanine
11 4 19 D Aspartic acid
14 4 22 G Glycine
22 17 21 L Leucine
3 6 5 M Methionine
9 6 17 F Phenylalanine
5 5 19 Y Tyrosine
17 5 8 V Valine 

4ESE_1|Chain A|FMN-dependent NADH-azoreductase|Yersinia pestis (214092)
>7FCJ_1|Chain A|SIGIRR protein|Danio rerio (7955)
>4AFB_1|Chain A|EPA1P|CANDIDA GLABRATA (5478)
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 \(w=f(c)\)
4ESE , Knot 95 204 0.82 38 148 201 
SNAMSKVLVLKSSILATSSQSNQLADFFVEQWQAAHAGDQITVRDLAAQPIPVLDGELVGALRPSGTALTPRQQEALALSDELIAELQANDVIVIAAPMYNFNIPTQLKNYFDMIARAGVTFRYTEKGPEGLVTGKRAIILTSRGGIHKDTPTDLVVPYLRLFLGFIGITDVEFVFAEGIAYGPEVATKAQADAKTLLAQVVAA
7FCJ , Knot 72 155 0.78 40 114 148 
MKMYDAYISYVNNENDRKFVNFILKPHLENKYSHKLLLNDTNILPGAEPSAELLMNISRCQRLIVVLSQSYLEQEWCTTNFRQGLWHLIELSRKPIFIIFQSQQKQISQDISQQLRQHQPSITMITWGAHSMTPSSGFWKELALVMPRKHHHHHH
4AFB , Knot 115 262 0.81 40 165 251 
MGSSHHHHHHSSGLVPRGSHMTSSNDISLASKDPTTFPLGCSPDITTPKKGLSMELYSYDFRKKGSYPCWDAAYLDPNYPRTGYKSHRLLAKVDGVTGNINFYYHATKGCTPQLGHLPASYNYPKPLTMTNFTMLLYGYFRPKVTGFHTFTISADDLLFVNFGAGNAFDCCRRDSSADHFGNYQAYAIWGSKTAKDELTVHLDAGVYYPIRLFYNNIGKDGALSFTFKTESNENTVSDFSEYFFSLDDTEEGCPGLISYDSS

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 \(c\).

\(|P_{f(4ESE_1)}(2) \setminus P_{f(7FCJ_1)}(2)|=97\), \(|P_{f(7FCJ_1)}(2) \setminus P_{f(4ESE_1)}(2)|=63\). 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 1:001100111100011100000001101110010110110010100111011111010111110101011010000111100011101010011111111001011001000101110111010000011011101001111000111000010011110101111111100101111011101101100101010011101111
Pair \(Z_2\) Length of longest common subsequence
4ESE_1,7FCJ_1 160 3
4ESE_1,4AFB_1 163 3
7FCJ_1,4AFB_1 175 6

Newick tree

 
[
	4AFB_1:86.01,
	[
		4ESE_1:80,7FCJ_1:80
	]:6.01
]

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 \((0.85)(0.8)(\frac{359 }{\log_{20} 359}-\frac{155}{\log_{20}155})=61.6\)
Status Protein1 Protein2 d d1/2
Query variables 4ESE_1 7FCJ_1 80 69.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]