CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8IMI_1 1CPQ_1 5NIW_1 Letter Amino acid
3 2 3 C Cysteine
16 4 10 M Methionine
57 5 18 F Phenylalanine
86 2 21 R Arginine
50 10 36 D Aspartic acid
6 2 19 H Histidine
70 3 26 I Isoleucine
61 12 16 K Lycine
79 4 36 S Serine
47 2 32 N Asparagine
83 10 30 E Glutamic acid
57 2 27 Y Tyrosine
74 5 45 V Valine
94 31 57 A Alanine
56 7 42 T Threonine
88 8 49 L Leucine
66 3 25 P Proline
5 1 10 W Tryptophan
58 2 22 Q Glutamine
80 14 57 G Glycine 

8IMI_1|Chain A[auth 0]|ApcE|Anthocerotibacter panamensis (2857077)
>1CPQ_1|Chain A|CYTOCHROME C'|Rhodobacter capsulatus (1061)
>5NIW_1|Chain A|Glucose oxidase|Aspergillus niger (5061)
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 \(w=f(c)\)
8IMI , Knot 385 1136 0.79 40 294 928 
MPIKGTSGSNIARPRFYNTVMVETIEGANAEERYFNPGELSSMAGFFNDAQRRLAIVQILTTNAEAIVSRAAGRIFTGGSPMAFSVQQANRQKDAEKERVSARVVQAESEQPIGNEVVIEDKGGFLERLKSFFSYGGAEVETPGFRPIPIAVYGPERMQKSLRDLDWFLRYVNYSLVAGDSNMILLNCLGLREILEKACSIDATIVAVQEMRRAATGYLKSNDDKELVGSYFDVIIRSLNADKSDTPADVVRPSSPDRAGLVLPAIYALAGQSRPAFKMSRTLTSAEKERVVRAAYRQVFERDILAYGQSISYLDSKVKNGEISVKEFIRLLGKSELYRKQFFEPFINSRVLELAFKHFLGRAPESRTEVQNYYSIVAAQGLGGLVDALVDGEEYGRIFGEDTVPFIRDLGQEAQPSWNWGAAYSLYNYAAPRRKVPQFITLYADYVKPLPNQHPYGSGNDPLEIQFGAIFKSETKAPSARPAPIGKDVQRILIRSGNPITNERGNPAGGISDKTSLSPQIFKLTQDNRRIRGKSGKGSLITNAGAGSVEVNVQAVIRAAYQQVFGRQLYEGQHLSVSEIKLENGEISVKEFVRDLATSEIFRKLYWQNFYVCKSIEYIHRRLLGRPTYGRDETNRYYDLAFKKGFAGVVNAILDTMEYAEVFGDDVVPYERYVTPAGLNLRKLRAGTVPTLPSFEETPKFIEKGTAPDRALPQIRSAINQGVSKKRDQRKIFSTVGIQTSLASRTEFDALIRAAYRQVFERDMDSYRITEVFSVLETKLRNREITTKEFIQALASSDLYRKQFFEPYPPTKNVELSLKHLLGRATKDQAELRKYNQIIATQGFKPFINAILDSKEYGEVFGDGTVPYNRYPTLPAANFPNTEILYNQLTKQSAEVVVPSFKPVTSPRGMDMSQTPLMLQAMGDIAEAEQEVALQKPLFIQKGKALRGAEGDPYTIGTRRSPKPIFWVPQGGTNPTEFQNVIRAAYRQVFERDVPDYQRLSYPESRLKNGEISMREFIRQLAESDLYRKQFYEPYPNTKVIELLTKHFLGRAPQDQAEIQRYNRILAGKGLKVAIEEVLNSDEYTQLFGEDVVPFKRYPTLPTGTYLASVATNDEMIQQSGSSYSPSYAGYSYPFS
1CPQ , Knot 60 129 0.75 40 90 120 
ADTKEVLEAREAYFKSLGGSMKAMTGVAKAFDAEAAKVEAAKLEKILATDVAPLFPAGTSSTDLPGQTEAKAAIWANMDDFGAKGKAMHEAGGAVIAAANAGDGAAFGAALQKLGGTCKACHDDYREED
5NIW , Knot 233 581 0.85 40 268 545 
GIEASLLTDPKDVSGRTVDYIIAGGGLVGLTTAAKLTENPNISVLVIESGSYESDRGPIIEDLNAYGDIFGSSVDHAYETVELATNNQTALVRSGNGLGGSTLINGGTWTRPHKAQVDSWETVFGNEGWNWDNVAAYSLQAERARAPNAKQIAAGHYFNTSCHGVNGTVHAGPRDTGDDYSPIVKALMSAVEDRGVPTKKDFGCGDPHGVSMFPNTLHEDQVRSDAAREWLLPNYQRPNLQVLTGQYVGKVLLSQNGTTPRAVGVEFGTHKGNTHNVYAKHEVLLAAGSAVSPTILEYSGIGMKSILEPLGIDTVVDLPVGLNLQDQTTATVRSRITSAGAGQGQAAWFATFNETFGDYSEKAHELLNTKLEQWAEEAVARGGFHNTTALLIQYENYRDWIVNHNVAYSELFLDTAGVASFDVWDLLPFTRGYVHILDKDPYLHHFAYDPQYFLNELDLLGQAAATQLARNISNSGAMQTYFAGETIPGDNLAYDADLSAWTEYIPYHFRPNYHGVGTCSMMPKEMGGVVDNAARVYGVQGLRVIDGSIPPTQVSSHVMTVFYAMALKISDAILEDYASMQ

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 \(c\).

\(|P_{f(8IMI_1)}(2) \setminus P_{f(1CPQ_1)}(2)|=216\), \(|P_{f(1CPQ_1)}(2) \setminus P_{f(8IMI_1)}(2)|=12\). 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 1:11101001001101010001110010110100001011010011111001000111101100010111001110110110111101001000001000010101101000011100111000111100100110011101001110111111011001000100101110010001111000111100111001100100101011110010011010100000001110010111001010000011011010010011111111011110001110100010010000110110001100011101001001000100101010011011100010000110111000110111001110110000010000011110111111011101000101110001111001100101010111100100011100011011010100101110001010100110101111100000110101111100100111001011000010111110000010101101000000101001010110011110101010111011000111001001001010010100101010011001100011001010010100010010001110100100000000011100111111011100100101110011100001011110100101101101101000101100101100111010011001100000000110011100011000010111011000110001000010011011000100001000011011100010000110101100010101001110100001010000011100110111011100000101110101100001011110110001100010000101111010110010110100011110111011010001110011110010110110101001100001011111101100100100110110001100011000010010001001010100110011000100001001010001101100011101100010100000111101101110011000000011100111100010110100110110000110001000010011000110
Pair \(Z_2\) Length of longest common subsequence
8IMI_1,1CPQ_1 228 4
8IMI_1,5NIW_1 120 5
1CPQ_1,5NIW_1 202 4

Newick tree

 
[
	1CPQ_1:11.43,
	[
		8IMI_1:60,5NIW_1:60
	]:59.43
]

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 \((0.85)(0.8)(\frac{1265 }{\log_{20} 1265}-\frac{129}{\log_{20}129})=306.\)
Status Protein1 Protein2 d d1/2
Query variables 8IMI_1 1CPQ_1 366 203
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]