CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8JNN_1 6QEO_1 5GTH_1 Letter Amino acid
1 8 5 C Cysteine
1 7 10 W Tryptophan
1 6 11 H Histidine
28 3 2 K Lycine
14 22 23 S Serine
25 27 21 V Valine
42 17 34 A Alanine
3 16 23 N Asparagine
24 4 15 E Glutamic acid
24 18 31 L Leucine
8 2 11 M Methionine
21 7 14 P Proline
5 11 14 Y Tyrosine
16 12 13 R Arginine
7 15 8 Q Glutamine
31 25 31 G Glycine
9 19 16 T Threonine
21 8 8 D Aspartic acid
5 10 27 I Isoleucine
7 3 27 F Phenylalanine 

8JNN_1|Chain A|LPP1|Porphyridium purpureum (35688)
>6QEO_1|Chain A|Chymotrypsin-like elastase family member 1|Sus scrofa (9823)
>5GTH_1|Chains A, U[auth a]|Photosystem II protein D1|Thermosynechococcus vulcanus (32053)
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 \(w=f(c)\)
8JNN , Knot 124 293 0.80 40 153 273 
MEAFVPGVGPLLGAPAAPLAAVDVRCRHASVARRARVAVRMADDGFADLQPGDPGYKPKAKEMVKVSELGVSPFSDDANSVTRLGEGRLDEIAKDIMEGKKTGAEIKADLKKQAPAKPAAPAKKPEKKSGLASAKDAAGSAMGAVQRAVGSGKRGLDLLREDFLQTGPERAGVGRQDKTVDAPPQFGEPGYVTPAYQRVKVSSLGISVFEDDANAVTKVGGIKAVMEVAEKVASGELKTEEFEEGLKAGLSLDLALEKMEEEAAAGDLLPDYLKPLPEDTPRKGMTWKNYVGR
6QEO , Knot 107 240 0.81 40 163 230 
VVGGTEAQRNSWPSQISLQYRSGSSWAHTCGGTLIRQNWVMTAAHCVDRELTFRVVVGEHNLNQNDGTEQYVGVQKIVVHPYWNTDDVAAGYDIALLRLAQSVTLNSYVQLGVLPRAGTILANNSPCYITGWGLTRTNGQLAQTLQQAYLPTVDYAICSSSSYWGSTVKNSMVCAGGDGVRSGCQGDSGGPLHCLVNGQYAVHGVTSFVSRLGCNVTRKPTVFTRVSAYISWINNVIASN
5GTH , Knot 151 344 0.85 40 204 329 
MTTTLQRRESANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFAALGISTMAFNLNGFNFNHSVIDAKGNVINTWADIINRANLGMEVMHERNAHNFPLDLA

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 \(c\).

\(|P_{f(8JNN_1)}(2) \setminus P_{f(6QEO_1)}(2)|=84\), \(|P_{f(6QEO_1)}(2) \setminus P_{f(8JNN_1)}(2)|=94\). 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 1:10111111111111111111110100001011001011101100111010110110010100110100111011000100100110101001100110100011010101000111011111001000011101001110111110011101001101100011001100111100000101110110110101100010100111011000101100111101110110011010100001001101110101110010001111011100101110001001101000110
Pair \(Z_2\) Length of longest common subsequence
8JNN_1,6QEO_1 178 3
8JNN_1,5GTH_1 183 4
6QEO_1,5GTH_1 161 4

Newick tree

 
[
	8JNN_1:93.28,
	[
		6QEO_1:80.5,5GTH_1:80.5
	]:12.78
]

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 \((0.85)(0.8)(\frac{533 }{\log_{20} 533}-\frac{240}{\log_{20}240})=83.7\)
Status Protein1 Protein2 d d1/2
Query variables 8JNN_1 6QEO_1 106 98
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]