CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5KGV_1 2PHH_1 5SVN_1 Letter Amino acid
2 5 7 C Cysteine
3 34 33 G Glycine
0 18 29 I Isoleucine
0 46 29 L Leucine
0 17 15 P Proline
2 20 29 T Threonine
0 38 18 R Arginine
0 4 15 N Asparagine
0 19 32 D Aspartic acid
0 15 16 Q Glutamine
0 34 21 E Glutamic acid
0 12 37 K Lycine
0 19 19 S Serine
0 28 26 V Valine
2 36 27 A Alanine
0 9 20 H Histidine
0 6 11 M Methionine
0 12 20 F Phenylalanine
0 6 8 W Tryptophan
0 16 12 Y Tyrosine 

5KGV_1|Chain A|DNA/RNA (5'-D(*AP*TP*GP*GP*A)-R(P*G)-D(P*CP*TP*C)-3')|synthetic construct (32630)
>2PHH_1|Chain A|P-HYDROXYBENZOATE HYDROXYLASE|Pseudomonas fluorescens (294)
>5SVN_1|Chains A, B|Isocitrate dehydrogenase [NADP], mitochondrial|Homo sapiens (9606)
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 \(w=f(c)\)
5KGV , Knot 6 9 0.48 8 8 7 
ATGGAGCTC
2PHH , Knot 163 394 0.82 40 217 371 
MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAGVDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLTEKVEDWSDERFWTELKARLPAEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYEEIE
5SVN , Knot 180 424 0.85 40 234 405 
ADKRIKVAKPVVEMDGDEMTRIIWQFIKEKLILPHVDIQLKYFDLGLPNRDQTDDQVTIDSALATQKYSVAVKCATITPDEARVEEFKLKKMWKSPNGTIRNILGGTVFREPIICKNIPRLVPGWTKPITIGKHAHGDQYKATDFVADRAGTFKMVFTPKDGSGVKEWEVYNFPAGGVGMGMYNTDESISGFAHSCFQYAIQKKWPLYMSTKNTILKAYDGRFKDIFQEIFDKHYKTDFDKNKIWYEHRLIDDMVAQVLKSSGGFVWACKNYDGDVQSDILAQGFGSLGLMTSVLVCPDGKTIEAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLIRFAQMLEKVCVETVESGAMTKDLAGCIHGLSNVKLNEHFLNTTDFLDTIKSNLDRALGRQSLEHHHHHHHH

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 \(c\).

\(|P_{f(5KGV_1)}(2) \setminus P_{f(2PHH_1)}(2)|=2\), \(|P_{f(2PHH_1)}(2) \setminus P_{f(5KGV_1)}(2)|=211\). 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 1:101111000
Pair \(Z_2\) Length of longest common subsequence
5KGV_1,2PHH_1 213 3
5KGV_1,5SVN_1 232 3
2PHH_1,5SVN_1 183 5

Newick tree

 
[
	5KGV_1:11.22,
	[
		2PHH_1:91.5,5SVN_1:91.5
	]:25.72
]

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 \((0.85)(0.8)(\frac{403 }{\log_{20} 403}-\frac{9}{\log_{20}9})=128.\)
Status Protein1 Protein2 d d1/2
Query variables 5KGV_1 2PHH_1 160 81.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: