CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
9FCB_1 3MRX_1 4PIN_1 Letter Amino acid
3 36 6 Y Tyrosine
6 62 23 V Valine
14 46 7 N Asparagine
8 9 2 C Cysteine
3 30 6 Q Glutamine
1 22 6 H Histidine
6 50 11 I Isoleucine
2 65 24 E Glutamic acid
3 38 13 F Phenylalanine
10 29 16 S Serine
6 12 5 W Tryptophan
12 63 46 A Alanine
11 63 26 R Arginine
8 79 39 L Leucine
2 36 12 P Proline
7 36 20 T Threonine
7 49 26 D Aspartic acid
12 48 23 G Glycine
6 48 7 K Lycine
2 21 5 M Methionine 

9FCB_1|Chain A|Lysozyme C|Gallus gallus (9031)
>3MRX_1|Chain A|Glycogen phosphorylase, muscle form|Oryctolagus cuniculus (9986)
>4PIN_1|Chains A, B|Histidine-specific methyltransferase EgtD|Mycobacterium smegmatis (1772)
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 \(w=f(c)\)
9FCB , Knot 66 129 0.82 40 104 127 
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
3MRX , Knot 321 842 0.85 40 316 773 
SRPLSDQEKRKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPAPDEKIP
4PIN , Knot 133 323 0.79 40 168 300 
GHMALSLANYLAADSAAEALRRDVRAGLTATQKSLPPKWFYDAVGSDLFDQITRLPEYYPTRTEAQILRTRSAEIISAAGADTLVELGSGTSEKTRMLLDAMRDAELLRRFIPFDVDAGVLRSAGAAIGAEYPGIEIDAVCGDFEEHLGKIPHVGRRLVVFLGSTIGNLTPAPRAEFLSTLADTLQPGDSLLLGTDLVKDTGRLVRAYDDAAGVTAAFNRNVLAVVNRELSADFDLDAFEHVAKWNSDEERIEMWLRARTAQHVRVAALDLEVDFAAGEEMLTEVSCKFRPENVVAELAEAGLRQTHWWTDPAGDFGLSLAVR

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 \(c\).

\(|P_{f(9FCB_1)}(2) \setminus P_{f(3MRX_1)}(2)|=17\), \(|P_{f(3MRX_1)}(2) \setminus P_{f(9FCB_1)}(2)|=229\). 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
9FCB_1,3MRX_1 246 3
9FCB_1,4PIN_1 170 3
3MRX_1,4PIN_1 184 4

Newick tree

 
[
	3MRX_1:11.41,
	[
		9FCB_1:85,4PIN_1:85
	]:30.41
]

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 \((0.85)(0.8)(\frac{971 }{\log_{20} 971}-\frac{129}{\log_{20}129})=233.\)
Status Protein1 Protein2 d d1/2
Query variables 9FCB_1 3MRX_1 299 171
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]