CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7UUD_1 3CDT_1 1CMO_1 Letter Amino acid
17 5 6 F Phenylalanine
13 3 9 P Proline
17 10 7 D Aspartic acid
11 13 5 K Lycine
12 2 1 C Cysteine
7 1 3 H Histidine
24 11 12 T Threonine
27 9 14 V Valine
17 15 11 A Alanine
11 12 11 R Arginine
26 11 8 G Glycine
11 10 4 I Isoleucine
10 5 2 M Methionine
3 3 1 W Tryptophan
14 5 2 Q Glutamine
9 8 5 E Glutamic acid
16 6 6 S Serine
11 6 2 Y Tyrosine
21 13 8 N Asparagine
29 16 10 L Leucine 

7UUD_1|Chain A|3C-like proteinase nsp5|Severe acute respiratory syndrome coronavirus 2 (2697049)
>3CDT_1|Chain A|Lysozyme|Bacteriophage T4
>1CMO_1|Chain A|POLYOMAVIRUS ENHANCER BINDING PROTEIN 2|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 \(w=f(c)\)
7UUD , Knot 134 306 0.83 40 196 290 
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ
3CDT , Knot 78 164 0.80 40 119 156 
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRNCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL
1CMO , Knot 65 127 0.82 40 105 123 
VEVLADHPGELVRTDSPNFLCSVLPTHWRSNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRNATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRR

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 \(c\).

\(|P_{f(7UUD_1)}(2) \setminus P_{f(3CDT_1)}(2)|=126\), \(|P_{f(3CDT_1)}(2) \setminus P_{f(7UUD_1)}(2)|=49\). 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 1:011001111010101011010010001011110011001001100000110100001110000001110110101011100100011010100101001000110101100101110001010110001101010101011010010111010000101001001011011011001010101111000010111000010101111101111010011100100010010111100000110000101111101001111101010100110011010011101110001011011000011010
Pair \(Z_2\) Length of longest common subsequence
7UUD_1,3CDT_1 175 3
7UUD_1,1CMO_1 169 4
3CDT_1,1CMO_1 154 4

Newick tree

 
[
	7UUD_1:88.81,
	[
		1CMO_1:77,3CDT_1:77
	]:11.81
]

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 \((0.85)(0.8)(\frac{470 }{\log_{20} 470}-\frac{164}{\log_{20}164})=90.1\)
Status Protein1 Protein2 d d1/2
Query variables 7UUD_1 3CDT_1 113 86.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]