CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3VKN_1 1FHF_1 7SPH_1 Letter Amino acid
9 20 5 D Aspartic acid
16 16 9 I Isoleucine
12 17 8 V Valine
5 3 9 H Histidine
10 3 19 K Lycine
10 20 6 F Phenylalanine
4 5 3 Y Tyrosine
5 18 18 A Alanine
10 30 2 N Asparagine
5 13 5 Q Glutamine
6 9 14 E Glutamic acid
11 35 18 L Leucine
4 3 3 M Methionine
1 1 2 W Tryptophan
8 15 4 R Arginine
2 8 2 C Cysteine
12 23 10 G Glycine
9 17 4 P Proline
7 22 6 S Serine
7 26 5 T Threonine 

3VKN_1|Chains A, B|Galectin-8|Homo sapiens (9606)
>1FHF_1|Chains A, B, C|SEED COAT PEROXIDASE|Glycine max (3847)
>7SPH_1|Chain A|Myoglobin|Physeter macrocephalus (9755)
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 \(w=f(c)\)
3VKN , Knot 72 153 0.79 40 115 146 
MMLSLNNLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSMKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSF
1FHF , Knot 132 304 0.82 40 182 287 
QLTPTFYRETCPNLFPIVFGVIFDASFTDPRIGASLMRLHFHDCFVQGCDGSVLLNNTDTIESEQDALPNINSIRGLDVVNDIKTAVENSCPDTVSCADILAIAAEIASVLGGGPGWPVPLGRRDSLTANRTLANQNLPAPFFNLTQLKASFAVQGLNTLDLVTLSGGHTFGRARCSTFINRLYNFSNTGNPDPTLNTTYLEVLRARCPQNATGDNLTNLDLSTPDQFDNRYYSNLLQLNGLLQSDQELFSTPGADTIPIVNSFSSNQNTFFSNFRVSMIKMGNIGVLTGDEGEIRLQCNFVNG
7SPH , Knot 76 154 0.82 42 117 148 
MVLSEXEWQLVLHVWAKVEADVAGHGQDILIRLFKSXPETLEKFDRFKHLKTEAEMKASEDLKKVGVTALTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISCAIIEVLHSRHPGNFGACAQGAMNKALELFRKDIAAKYKELGYQG

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 \(c\).

\(|P_{f(3VKN_1)}(2) \setminus P_{f(1FHF_1)}(2)|=49\), \(|P_{f(1FHF_1)}(2) \setminus P_{f(3VKN_1)}(2)|=116\). 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 1:111010010011001111111011001011011110101100100101010010010101011101010100110110001100011000100001100000101111110001011101000110100111001001110101010011101
Pair \(Z_2\) Length of longest common subsequence
3VKN_1,1FHF_1 165 3
3VKN_1,7SPH_1 164 4
1FHF_1,7SPH_1 187 3

Newick tree

 
[
	1FHF_1:90.13,
	[
		3VKN_1:82,7SPH_1:82
	]:8.13
]

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 \((0.85)(0.8)(\frac{457 }{\log_{20} 457}-\frac{153}{\log_{20}153})=90.0\)
Status Protein1 Protein2 d d1/2
Query variables 3VKN_1 1FHF_1 111 83
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]