CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1LJH_1 6LZM_1 5NJS_1 Letter Amino acid
2 5 2 M Methionine
3 6 3 Y Tyrosine
3 5 3 Q Glutamine
12 11 12 G Glycine
6 13 6 K Lycine
6 9 6 V Valine
2 8 2 E Glutamic acid
14 12 14 N Asparagine
8 16 8 L Leucine
12 15 12 A Alanine
7 10 7 D Aspartic acid
8 2 8 C Cysteine
1 1 1 H Histidine
6 10 6 I Isoleucine
3 5 3 F Phenylalanine
2 3 2 P Proline
10 6 10 S Serine
11 13 11 R Arginine
6 3 6 W Tryptophan
7 11 7 T Threonine 

1LJH_1|Chains A, B|Lysozyme C|Gallus gallus (9031)
>6LZM_1|Chain A|T4 LYSOZYME|Enterobacteria phage T4 (10665)
>5NJS_1|Chain A|Lysozyme C|Gallus gallus (9031)
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 \(w=f(c)\)
1LJH , Knot 66 129 0.82 40 104 127 
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
6LZM , Knot 78 164 0.80 40 121 157 
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL
5NJS , Knot 66 129 0.82 40 104 127 
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL

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 \(c\).

\(|P_{f(1LJH_1)}(2) \setminus P_{f(6LZM_1)}(2)|=60\), \(|P_{f(6LZM_1)}(2) \setminus P_{f(1LJH_1)}(2)|=77\). 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
1LJH_1,6LZM_1 137 3
1LJH_1,5NJS_1 0 129
6LZM_1,5NJS_1 137 3

Newick tree

 
[
	6LZM_1:79.09,
	[
		1LJH_1:0,5NJS_1:0
	]:79.09
]

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 \((0.85)(0.8)(\frac{293 }{\log_{20} 293}-\frac{129}{\log_{20}129})=51.0\)
Status Protein1 Protein2 d d1/2
Query variables 1LJH_1 6LZM_1 63 56
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]