CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3HQA_1 6YAG_1 7XOI_1 Letter Amino acid
4 4 17 R Arginine
4 14 21 Q Glutamine
1 4 41 P Proline
0 3 9 W Tryptophan
3 17 33 N Asparagine
7 0 4 C Cysteine
5 13 26 I Isoleucine
4 16 38 L Leucine
2 1 7 M Methionine
2 16 40 T Threonine
8 41 39 A Alanine
3 23 49 D Aspartic acid
5 22 31 E Glutamic acid
3 35 40 G Glycine
8 29 17 K Lycine
2 11 34 Y Tyrosine
2 8 13 H Histidine
1 14 31 F Phenylalanine
4 26 25 S Serine
5 33 33 V Valine 

3HQA_1|Chains A, B|Complement C5|Homo sapiens (9606)
>6YAG_1|Chains A, B, C, D|Lipoprotein|Streptococcus pneumoniae (1313)
>7XOI_1|Chains A, C, E, G, I, K, M, O|alpha-glucosidase N-terminal polypeptide|Aspergillus sojae NBRC 4239 (927772)
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 \(w=f(c)\)
3HQA , Knot 41 73 0.80 38 63 71 
MLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISLGPRCIKAFTECCVVASQLRANISHKDMQLG
6YAG , Knot 135 330 0.79 38 168 299 
SSHHHHHHMSGENLYFQGASAAIVTDTGGVDDKSFNQSAWEGLQAWGKEHNLSKDNGFTYFQSTSEADYANNLQQAAGSYNLIFGVGFALNNAVKDAAKEHTDLNYVLIDDVIKDQKNVASVTFADNESGYLAGVAAAKTTKTKQVGFVGGIESEVISRFEAGFKAGVASVDPSIKVQVDYAGSFGDAAKGKTIAAAQYAAGADIVYQVAGGTGAGVFAEAKSLNESRPENEKVWVIGVDRDQEAEGKYTSKDGKESNFVLVSTLKQVGTTVKDISNKAERGEFPGGQVIVYSLKDKGVDLAVTNLSEEGKKAVEDAKAKILDGSVKVPE
7XOI , Knot 221 548 0.84 40 271 516 
APVNTTTEDETAQIPAEAVIGYSDLEGDFDVAVLPFSNSTNNGLLFINTTIASIAAKEEGVSLEKREAEAEFQSKDGVEDLDGPGDDLYVKDLSGCPGYKATKHWQTRSGFYADLTLAGPACNVFGTDLPDLKLEVEYQTSDRLHVKILDTNNTVYQVPDSVFPRPGFGEWCSPKDSKLKFDFQADPFSFTVSRTDTGEVLFDTTGNKLVFESQYVYLKTHLPQNPHLYGLGEHSDAFMLNTTNYTRTIYTRDAYGTPQGENLYGAHPIYFDHRQTGTHGVFLLNSNGMDIFIDNNATQYLEYNIIGGVLDFYFIAGPSPRDVAIQYAEITQTPLMTPYWGLGYHQCKYGYQDVYEVAAVVANYSTNNIPLETIWTDIDYMDRRRIFTIDPERFPANLYKDLVDTIHARDQHYIVMVDPAVYYKESNPALDEGLRYDIFMKENNGSEYQGVVWAGPSHFPDWFHPDSQQYWSEQFLAFFDGTNGPDIDALWIDMNEPANFYNRPYPGNNTTPENFAEVDGDPPAAPAVRDGPDAPIPGFPASLQPNWV

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 \(c\).

\(|P_{f(3HQA_1)}(2) \setminus P_{f(6YAG_1)}(2)|=38\), \(|P_{f(6YAG_1)}(2) \setminus P_{f(3HQA_1)}(2)|=143\). 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 1:1100010011100000110000001101000000000110101110010110000111001010100001011
Pair \(Z_2\) Length of longest common subsequence
3HQA_1,6YAG_1 181 3
3HQA_1,7XOI_1 248 4
6YAG_1,7XOI_1 175 5

Newick tree

 
[
	3HQA_1:11.71,
	[
		6YAG_1:87.5,7XOI_1:87.5
	]:27.21
]

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 \((0.85)(0.8)(\frac{403 }{\log_{20} 403}-\frac{73}{\log_{20}73})=102.\)
Status Protein1 Protein2 d d1/2
Query variables 3HQA_1 6YAG_1 122 74.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: