CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1QTK_1 5EHG_1 5VQD_1 Letter Amino acid
8 5 10 C Cysteine
8 23 55 L Leucine
3 5 19 F Phenylalanine
10 18 38 S Serine
3 8 18 Y Tyrosine
14 14 21 N Asparagine
12 27 41 G Glycine
1 8 18 H Histidine
2 10 23 M Methionine
2 15 32 P Proline
12 6 33 A Alanine
3 5 17 Q Glutamine
7 20 32 T Threonine
6 6 9 W Tryptophan
6 22 32 V Valine
11 19 30 R Arginine
7 9 34 D Aspartic acid
2 23 39 E Glutamic acid
6 12 35 I Isoleucine
6 21 37 K Lycine 

1QTK_1|Chain A|LYSOZYME|Gallus gallus (9031)
>5EHG_1|Chains A, B[auth C]|RNA-directed RNA polymerase NS5|Dengue virus type 3 (strain Philippines/H87/1956) (408870)
>5VQD_1|Chain A|Beta-glucoside phosphorylase BglX|unidentified (32644)
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 \(w=f(c)\)
1QTK , Knot 66 129 0.82 40 104 127 
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
5EHG , Knot 120 276 0.81 40 176 263 
GTGSQGETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAVSRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTVEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVRNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVDLGAGTRHVNAEPETPNMDVI
5VQD , Knot 234 573 0.86 40 274 539 
MYESILSIKPYNLSKEQITWVNQTLVSLSDDEKLGQLICEIIWDKPGCDPLDVMKHFLPGAVMYRPFKAKRMREFTQRLQKASKIPLLIACNLERGGSGGNGGMEDGTYVASPMGVAATDDESSAEHLGEVCASEGSAVGVNWTYEPIIDIDMNPENPITNVRTYGSDPERIIRMAKAYCRGCRKWGVLTTIKHFPGDGVDYRDQHLMSSVNNLSADEWMDTYGRIYQALIEDGAETLMSAHIRQPNVTRMVNPLIKDEEIMPGSLSKELMQGILRGRFHFNGLICTDATQMVGYTCSMPRHEALPTSIQNGADMLTFTLNPTEDFKALQEGLSCGLLTHERLDEAVARILGMKAKLRLPERKDVVPPLHAMERIQSKKHKKWALEIADESITLVKDKQKGLLPLSPQKTKRIILVQATNEKPEGGYLSEARLFKGLLEKEGFIVHWFEEVPRPGTGYSIEDLKRDTDLFIYYANFKVSSNQTTIRLVWSDFLGDSSPKFVCDVPTLFLSFSNPYHLVDVPMVKTYINAYTSNEATVRMMIEKLMGRSSFKGKSPVDPFAGLWDARLHHHHHH

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 \(c\).

\(|P_{f(1QTK_1)}(2) \setminus P_{f(5EHG_1)}(2)|=53\), \(|P_{f(5EHG_1)}(2) \setminus P_{f(1QTK_1)}(2)|=125\). 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 1:011100011111000110000100110110110100010001000000100001110100011000100110001001100111000101010010011001011011111000001001011101001
Pair \(Z_2\) Length of longest common subsequence
1QTK_1,5EHG_1 178 3
1QTK_1,5VQD_1 224 4
5EHG_1,5VQD_1 192 4

Newick tree

 
[
	5VQD_1:10.93,
	[
		1QTK_1:89,5EHG_1:89
	]:19.93
]

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 \((0.85)(0.8)(\frac{405 }{\log_{20} 405}-\frac{129}{\log_{20}129})=83.3\)
Status Protein1 Protein2 d d1/2
Query variables 1QTK_1 5EHG_1 108 78.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]