CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4ZFP_1 7JFQ_1 7KVC_1 Letter Amino acid
6 11 25 K Lycine
2 13 10 P Proline
11 11 21 R Arginine
12 26 25 G Glycine
8 29 35 L Leucine
6 27 19 V Valine
14 21 23 N Asparagine
8 12 3 C Cysteine
3 11 19 Y Tyrosine
7 17 26 D Aspartic acid
1 7 14 H Histidine
7 24 24 T Threonine
6 11 32 I Isoleucine
2 10 7 M Methionine
3 17 16 F Phenylalanine
10 16 30 S Serine
6 3 2 W Tryptophan
12 17 8 A Alanine
3 14 18 Q Glutamine
2 9 31 E Glutamic acid 

4ZFP_1|Chain A|Lysozyme C|Gallus gallus (9031)
>7JFQ_1|Chain A|3C-like proteinase|Severe acute respiratory syndrome coronavirus 2 (2697049)
>7KVC_1|Chains A, B, C, D, E, F, G, H, I, J|p9-1|Mal de Rio Cuarto virus (185954)
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 \(w=f(c)\)
4ZFP , Knot 66 129 0.82 40 104 127 
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
7JFQ , Knot 134 306 0.83 40 196 290 
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ
7KVC , Knot 158 388 0.81 40 215 360 
MRGSHHHHHHGMASMTGGQQMGRDLYDDDDKDRWGSELEICSWYHGGRGNSIADLERRTFGSYKIEEITIKNDQQQKTTNQQQISNNEQRISTKKIPILDDGIFDLINYLLNGTHFDKTHYCGFDYSHLPTLERDFNTASNYVSENYSIIVEEIDLNKYERSESISLKSPDFTVVLEYFKKHVEGQTEQEENKTESTSSELPAKIVRELPLLPIMCRESEDSISEDILEGEGAVIQVLKMFMKGFLVHLGENPNSYDRQLTIEKYRPLLISIIGYEFTVGTRATHTKINHIYYQLATFDNYPFDLLRFQLQSLIDTPNVIKERIEKDGLFKVITTTNARGQYQSVLLRGINGSESYLNLKRYRKFKVRVVGNVDNVIKNDFSSLKLDV

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 \(c\).

\(|P_{f(4ZFP_1)}(2) \setminus P_{f(7JFQ_1)}(2)|=43\), \(|P_{f(7JFQ_1)}(2) \setminus P_{f(4ZFP_1)}(2)|=135\). 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 1:011100011111000110000100110110110100010001000000100001110100011000100110001001100111000101010010011001011011111000001001011101001
Pair \(Z_2\) Length of longest common subsequence
4ZFP_1,7JFQ_1 178 4
4ZFP_1,7KVC_1 195 3
7JFQ_1,7KVC_1 171 3

Newick tree

 
[
	4ZFP_1:95.81,
	[
		7JFQ_1:85.5,7KVC_1:85.5
	]:10.31
]

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 \((0.85)(0.8)(\frac{435 }{\log_{20} 435}-\frac{129}{\log_{20}129})=91.7\)
Status Protein1 Protein2 d d1/2
Query variables 4ZFP_1 7JFQ_1 120 84
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]