CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5IIX_1 5UTX_1 4DDA_1 Letter Amino acid
58 31 12 A Alanine
11 14 14 N Asparagine
18 35 12 G Glycine
19 8 1 H Histidine
30 11 3 F Phenylalanine
30 7 2 P Proline
61 14 6 K Lycine
27 21 7 T Threonine
1 1 6 W Tryptophan
17 9 3 Y Tyrosine
41 22 7 D Aspartic acid
58 22 2 E Glutamic acid
65 28 8 L Leucine
30 17 10 S Serine
30 22 6 V Valine
21 14 11 R Arginine
35 4 8 C Cysteine
17 10 3 Q Glutamine
14 18 6 I Isoleucine
0 11 2 M Methionine 

5IIX_1|Chain A|Serum albumin|Equus caballus (9796)
>5UTX_1|Chains A, B|Thioredoxin reductase|Vibrio vulnificus CMCP6 (216895)
>4DDA_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 \(w=f(c)\)
5IIX , Knot 223 583 0.81 38 238 529 
DTHKSEIAHRFNDLGEKHFKGLVLVAFSQYLQQCPFEDHVKLVNEVTEFAKKCAADESAENCDKSLHTLFGDKLCTVATLRATYGELADCCEKQEPERNECFLTHKDDHPNLPKLKPEPDAQCAAFQEDPDKFLGKYLYEVARRHPYFYGPELLFHAEEYKADFTECCPADDKLACLIPKLDALKERILLSSAKERLKCSSFQNFGERAVKAWSVARLSQKFPKADFAEVSKIVTDLTKVHKECCHGDLLECADDRADLAKYICEHQDSISGKLKACCDKPLLQKSHCIAEVKEDDLPSDLPALAADFAEDKEICKHYKDAKDVFLGTFLYEYSRRHPDYSVSLLLRIAKTYEATLEKCCAEADPPACYRTVFDQFTPLVEEPKSLVKKNCDLFEEVGEYDFQNALIVRYTKKAPQVSTPTLVEIGRTLGKVGSRCCKLPESERLPCSENHLALALNRLCVLHEKTPVSEKITKCCTDSLAERRPCFSALELDEGYVPKEFKAETFTFHADICTLPEDEKQIKKQSALAELVKHKPKATKEQLKTVLGNFSAFVAKCCGAEDKEACFAEEGPKLVASSQLALA
5UTX , Knot 138 319 0.83 40 195 309 
MSDMKHSKLLILGSGPAGYTAAVYAARANLNPVLITGMQQGGQLTTTTEVENWPGDPEGLTGPGLMDRMKEHAERFETEIIFDHINEVDFSTRPFVLKGDAASYSCDALIISTGASAKYLGLESEEAFKGRGVSACATCDGFFYRNQKVAVVGGGNTAVEEALYLSNIAAEVHLIHRRDSFRAEKILINRLMDKVQNGNIVLHTDRVLDEVLGDEMGVTGVRLKDVKTGGTEELDVMGAFIAIGHSPNTQIFQGQLDMKDGYILVKSGLEGNATQTSVEGIFAAGDVMDHNYRQAITSAGTGCMAALDAERYLDSLNDK
4DDA , 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 \(c\).

\(|P_{f(5IIX_1)}(2) \setminus P_{f(5UTX_1)}(2)|=109\), \(|P_{f(5UTX_1)}(2) \setminus P_{f(5IIX_1)}(2)|=66\). 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 1:0000001100100110001011111110001000110001011001001100011000100000010011100100110101001011000000010000011000000101101010101001110001001110010011000101011011101000010100001100011011101011000111001000100001001100110110110100011010110100110010010000001011001000101100100000010101010000111000001101000011001111110110000100000010011110110000000100010111011000010100001010111000011001011100100110000011001100010011110000011010010110110011011000001100001100000111110010110000110001000000011000101011010010110010100101010100110000010000111011000101000010011101011110001100001011001101110001111
Pair \(Z_2\) Length of longest common subsequence
5IIX_1,5UTX_1 175 3
5IIX_1,4DDA_1 202 4
5UTX_1,4DDA_1 177 3

Newick tree

 
[
	4DDA_1:97.31,
	[
		5IIX_1:87.5,5UTX_1:87.5
	]:9.81
]

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 \((0.85)(0.8)(\frac{902 }{\log_{20} 902}-\frac{319}{\log_{20}319})=157.\)
Status Protein1 Protein2 d d1/2
Query variables 5IIX_1 5UTX_1 194 152.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]