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Statistics of GB-speckles, coding sequences of nucleotide sequences of omp1 gene of Chlamydia trachomatis, processed by s-LASCA technique S.S. Ulyanov.

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Presentation on theme: "Statistics of GB-speckles, coding sequences of nucleotide sequences of omp1 gene of Chlamydia trachomatis, processed by s-LASCA technique S.S. Ulyanov."— Presentation transcript:

1 Statistics of GB-speckles, coding sequences of nucleotide sequences of omp1 gene of Chlamydia trachomatis, processed by s-LASCA technique S.S. Ulyanov a, b, O.V. Ulianova b, S.S. Zaytsev b, Yu.V. Saltykov b, V.A. Feodorova b

2 AFFILIATION a Saratov State University, RUSSIA
b Federal Research Center for Virology and Microbiology, Branch in Saratov RUSSIA

3 ABSTRACT GB-speckles, simulated for nucleotide sequences of omp1 gene of Chlamydia trachomatis, have been processed by s-LASCA technique. Statistics of LASCA-images of GB-speckles has been analyzed. Perspectives of application of suggested technique in modern bioinformatics have been demonstrated.

4 Nucleotide sequence omp1 for E/Bour(E1) ATGAAAAAACTCTTGAAATCGGTATTAGTATTTGCCGCTTTGAGTTCTGCTTCCTCCTTGCAAGCTCTGCCTGTGGGGAATCCTGCTGAACCAAGCCTTATGATCGACGGAATTCTGTGGGAAGGTTTCGGCGGAGATCCTTGCGATCCTTGCACCACTTGGTGTGACGCTATCAGCATGCGTATGGGTTACTATGGTGACTTTGTTTTCGACCGTGTTTTGAAAACAGATGTGAATAAAGAATTCCAAATGGGTGACAAGCCTACAAGTACTACAGGCAATGCTACAGCTCCAACCACTCTTACAGCAAGAGAGAATCCTGCTTACGGCCGACATATGCAGGATGCTGAGATGTTTACAAATGCCGCTTGCATGGCATTGAATATTTGGGATCGCTTTGATGTATTCTGTACACTAGGAGCCTCTAGCGGATACCTTAAAGGAAACTCTGCTTCTTTCAATTTAGTTGGATTGTTTGGAGATAATGAAAATCAAAGCACGGTCAAAACGAATTCTGTACCAAATATGAGCTTAGATCAATCTGTTGTTGAACTTTACACAGATACTGCCTTCTCTTGGAGCGTGGGCGCTCGAGCAGCTTTGTGGGAGTGCGGATGTGCGACTTTAGGGGCTTCTTTCCAATACGCTCAATCTAAACCTAAAGTCGAAGAATTAAACGTTCTCTGTAACGCAGCTGAGTTTACTATCAATAAGCCTAAAGGATATGTAGGGCAAGAATTCCCTCTTGCACTCATAGCAGGAACTGATGCAGCGACGGGCACTAAAGATGCCTCTATTGATTACCATGAGTGGCAAGCAAGTTTAGCTCTCTCTTACAGATTGAATATGTTCACTCCCTACATTGGAGTTAAATGGTCTCGAGCAAGTTTTGATGCCGATACGATTCGTATAGCCCAGCCAAAATCAGCTACAGCTATCTTTGATACTACCACGCTTAACCCAACTATTGCTGGAGCTGGCGATGTGAAAGCTAGCGCAGAGGGTCAGCTCGGAGATACCATGCAAATCGTCTCCTTGCAATTGAACAAGATGAAATCTAGAAAATCTTGCGGTATTGCAGTAGGAACGACTATTGTAGATGCAGACAAATACGCAGTTACAGTTGAGACTCGCTTGATCGATGAGAGAGCTGCTCACGTAAATGCACAATTCCGCTTCTAA

5 Nucleotide sequence omp1 for E/IU-TC0755ut ATGAAAAAACTCTTGAAATCGGTATTAGTATTTGCCGCTTTGAGTTCTGCTTCCTCCTTGCAAGCTCTGCCTGTGGGGAATCCTGCTGAACCAAGCCTTATGATCGACGGAATTCTGTGGGAAGGTTTCGGCGGAGATCCTTGCGATCCTTGCACCACTTGGTGTGACGCTATCAGCATGCGTATGGGTTACTATGGTGACTTTGTTTTCGACCGTGTTTTGAAAACAGATGTGAATAAAGAATTCCAAATGGGTGACAAGCCTACAAGTACTACAGGCAATGCTACAGCTCCAACCACTCTTACAGCAAGAGAGAATCCTGCTTACGGCCGACATATGCAGGATGCTGAGATGTTTACAAATGCCGCTTGCATGGCATTGAATATTTGGGATCGCTTTGATGTATTCTGTACACTAGGAGCCTCTAGCGGATACCTTAAAGGAAACTCTGCTTCTTTCAATTTAGTTGGATTGTTTGGAGATAATGAAAATCAAAGCACGGTCAAAACGAATTCTGTACCAAATATGAGCTTAGATCAATCTGTTGTTGAACTTTACACAGATACTGCCTTCTCTTGGAGCGTGGGCGCTCGAGCAGCTTTGTGGGAGTGCGGATGTGCGACTTTAGGGGCTTCTTTCCAATACGCTCAATCTAAACCTAAAGTCGAAGAATTAAACGTTCTCTGTAACGCAGCTGAGTTTACTATCAATAAGCCTAAAGGATATGTAGGGCAAGAATTCCCTCTTGCACTCATAGCAGGAACTGATGCAGCGACGGGCACTAAAGATGCCTCTATTGATTACCATGAGTGGCAAGCAAGTTTAGCTCTCTCTTACAGATTGAATATGTTCACTCCCTACATTGGAGTTAAATGGTCTCGAGCAAGTTTTGATGCCGATACGATTCGTATAGCCCAGCCAAAATCAGCTACAGCTATCTTTGATACTACCACGCTTAACCCAACTATTGCTGGAGCTGGCGATGTGAAAGCTAGCACAGAGGGTCAGCTCGGAGATACCATGCAAATCGTCTCCTTGCAATTGAACAAGATGAAATCTAGAAAATCTTGCGGTATTGCAGTAGGAACGACTATTGTAGATGCAGACAAATACGCAGTTACAGTTGAGACTCGCTTGATCGATGAGAGAGCTGCTCACGTAAATGCACAATTCCGCTTCTAA

6 Comparison of the E/Bour(E1) and E/IU-TC0755ut omp1 nucleotide sequences

7 S. S. Ulyanov, S. S. Zaytsev, O. V. Ulianova,
Algorithm of re-coding of nucleotide sequences and generation of gene-based speckles (GB-speckles) is described in: S. S. Ulyanov, S. S. Zaytsev, O. V. Ulianova, Y. V. Saltykov, V. A. Feodorova, "Using of methods of speckle optics for Chlamydia trachomatis typing“, Proc. of SPIE, vol , D-1-9, (2017)

8 Three GB-speckle patterns are shown on the slides below
GB-speckle pattern for E/Bour(E1) GB-speckle pattern for E /IU-TC0755ut GB-speckle pattern for E /IU-TC0755ut with one “artificial” mutation. One deletion is introduced in the beginning of nucleotide sequence

9 GB-speckle pattern for the E/Bour(E1) omp1

10 GB-speckle pattern for the E /IU-TC0755ut omp1

11 GB-speckle pattern for the E/IU-TC0755ut omp1 with a single mutation
(Single Nucleotide Polymorphism, SNP)

12 Three phase map of GB-speckle patterns are shown below
GB-speckle pattern for E/Bour(E1) GB-speckle pattern for E /IU-TC0755ut GB-speckle pattern for E /IU-TC0755ut with one “artificial” mutation. One deletion is introduced in the beginning of nucleotide sequence

13 Phase structure of GB-speckles for the E/Bour(E1) omp1

14 Phase structure of GB-speckles for the E /IU-TC0755ut omp1

15 Phase structure of GB-speckles for the E/IU-TC0755ut with a single mutation (SNP)

16 s-LASCA processing of GB-speckles
s-LASCA is based on the analysis of a single realization of static speckles. In this case, the entire two-dimensional implementation of the speckle field is divided into small areas, usually with a size of 5x5 or 7x7 pixels. For each of the selected areas, the local contrast value of the static speckles is calculated, after which a LASCA image is constructed.

17 s-LASCA image for GB-speckles, generated for E/Bour(E1) nucleotide sequence. are demonstrated on next five slides. Size of subarea for speckle processing is varying.

18 Subarea size for s-LASCA imaging is 3 x 3 pixels.
s-LASCA image of GB-speckles, generated for the E/Bour(E1) omp1 nucleotide sequence. Subarea size for s-LASCA imaging is 3 x 3 pixels.

19 s-LASCA image of GB-speckles, generated for the E/Bour(E1) omp1
nucleotide sequence. Subarea size for s-LASCA imaging is 5 x 5 pixels.

20 s-LASCA image of GB-speckles, generated for the E/Bour(E1) omp1
nucleotide sequence. Subarea size for s-LASCA imaging is 7 x 7 pixels.

21 s-LASCA image of GB-speckles, generated for the E/Bour(E1) omp1
nucleotide sequence. Subarea size for s-LASCA imaging is 10 x 10 pixels.

22 Subarea size for s-LASCA imaging is 15 x 15 pixels.
s-LASCA image of GB-speckles, generated for the E/Bour(E1) omp1 nucleotide sequence. Subarea size for s-LASCA imaging is 15 x 15 pixels.

23 s-LASCA image, generated for GB-speckles, generated for E /IU-TC0755ut are demonstrated on next five slides. Size of subarea for speckle processing is varying.

24 s-LASCA image for GB-speckles, generated for E /IU-TC0755ut.
Subarea size for s-LASCA imaging is 3 x 3 pixels.

25 s-LASCA image for GB-speckles, generated for E /IU-TC0755ut.
Subarea size for s-LASCA imaging is 5 x 5 pixels.

26 s-LASCA image for GB-speckles, generated for E /IU-TC0755ut.
Subarea size for s-LASCA imaging is 7 x 7 pixels.

27 s-LASCA image for GB-speckles, generated for E /IU-TC0755ut.
Subarea size for s-LASCA imaging is 10 x 10 pixels.

28 s-LASCA image for GB-speckles, generated for E /IU-TC0755ut.
Subarea size for s-LASCA imaging is 15 x 15 pixels.

29 s-LASCA image, generated for E /IU-TC0755ut nucleotide sequence, having one mutation (deletion) are demonstrated on next four slides. Size of subarea for speckle processing is varying.

30 s-LASCA image of GB-speckles, generated for the E /IU-TC0755ut
nucleotide sequence, having one mutation (deletion). Subarea size for s-LASCA imaging is 3 x 3 pixels.

31 s-LASCA image of GB-speckles, generated for the E /IU-TC0755ut
nucleotide sequence, having one mutation (deletion). Subarea size for s-LASCA imaging is 5 x 5 pixels.

32 s-LASCA image of GB-speckles, generated for the E /IU-TC0755ut
nucleotide sequence, having one mutation (deletion). Subarea size for s-LASCA imaging is 7 x 7 pixels.

33 s-LASCA image of GB-speckles, generated for the E /IU-TC0755ut
nucleotide sequence, having one mutation (deletion). Subarea size for s-LASCA imaging is 10 x 10 pixels.

34 Results of mutual interference of GB-speckles, described above, is shown
on three next slides

35 Interference of GB-speckles, generated for the E/IU-TC0755ut and
the E/Bour(E1) omp1 nucleotide sequences

36 Interference of GB-speckles, generated for the E/IU-TC0755ut omp1 nucleotide sequence and 𝜋−phase shifted GB-speckles

37 Interference of GB-speckles, generated for omp1 nucleotide sequences of the E/IU-TC0755ut and the E/IU-TC0755ut with a single mutation (deletion)

38 s-LASCA image for interfering E /IU-TC0755ut GB-speckles and E/Bour(E1) GB-speckles are demonstrated on next five slides. Size of subarea for speckle processing is varying.

39 s-LASCA image for interfering of the omp1 E/IU-TC0755ut
GB-speckles and the omp1 E/Bour(E1) GB-speckles. Subarea size for s-LASCA imaging is 3 x 3 pixels.

40 s-LASCA image for interfering of the omp1 E/IU-TC0755ut
GB-speckles and the omp1 E/Bour(E1) GB-speckles. Subarea size for s-LASCA imaging is 5 x 5 pixels.

41 Subarea size for s-LASCA imaging is 7 x 7 pixels.
s-LASCA image for interfering E /IU-TC0755ut GB-speckles and E/Bour(E1) GB-speckles. Subarea size for s-LASCA imaging is 7 x 7 pixels.

42 s-LASCA image for interfering of the omp1 E/IU-TC0755ut
GB-speckles and the omp1 E/Bour(E1) GB-speckles. Subarea size for s-LASCA imaging is 10 x 10 pixels.

43 s-LASCA image for interfering of the omp1 E/IU-TC0755ut
GB-speckles and the omp1 E/Bour(E1) GB-speckles. Subarea size for s-LASCA imaging is 15 x 15 pixels.

44 s-LASCA image for interfering E /IU-TC0755ut GB-speckles and π-phase shifted GB-speckles (generated for the same nucleotide sequence) are demonstrated on next five slides. Size of subarea for speckle processing is varying.

45 Subarea size for s-LASCA imaging is 3 x 3 pixels.
s-LASCA image for interfering of the omp1 E/IU-TC0755ut GB-speckles and π-phase shifted GB-speckles (generated for the same nucleotide sequence). Subarea size for s-LASCA imaging is 3 x 3 pixels.

46 Subarea size for s-LASCA imaging is 5 x 5 pixels.
s-LASCA image for interfering of the omp1 E/IU-TC0755ut GB-speckles and π-phase shifted GB-speckles (generated for the same nucleotide sequence). Subarea size for s-LASCA imaging is 5 x 5 pixels.

47 Subarea size for s-LASCA imaging is 7 x 7 pixels.
s-LASCA image for interfering of the omp1 E/IU-TC0755ut GB-speckles and π-phase shifted GB-speckles (generated for the same nucleotide sequence). Subarea size for s-LASCA imaging is 7 x 7 pixels.

48 Subarea size for s-LASCA imaging is 10 x 10 pixels.
s-LASCA image for interfering of the omp1 E/IU-TC0755ut GB-speckles and π-phase shifted GB-speckles (generated for the same nucleotide sequence). Subarea size for s-LASCA imaging is 10 x 10 pixels.

49 Subarea size for s-LASCA imaging is 15 x 15 pixels.
s-LASCA image for interfering of the omp1 E/IU-TC0755ut GB-speckles and π-phase shifted GB-speckles (generated for the same nucleotide sequence). Subarea size for s-LASCA imaging is 15 x 15 pixels.

50 s-LASCA image for interfering E /IU-TC0755ut GB-speckles and GB-speckles, generated for the same nucleotide sequence with one mutation (deletion) are demonstrated on next five slides. Size of subarea for speckle processing is varying.

51 Subarea size for s-LASCA imaging is 3 x 3 pixels.
s-LASCA image for interfering of the omp1 E/IU-TC0755ut GB-speckles and GB-speckles, generated for the same nucleotide sequence with a single mutation (deletion). Subarea size for s-LASCA imaging is 3 x 3 pixels.

52 Subarea size for s-LASCA imaging is 5 x 5 pixels.
s-LASCA image for interfering of the omp1 E/IU-TC0755ut GB-speckles and GB-speckles, generated for the same nucleotide sequence with a single mutation (deletion). Subarea size for s-LASCA imaging is 5 x 5 pixels.

53 Subarea size for s-LASCA imaging is 7 x 7 pixels.
s-LASCA image for interfering of the omp1 E/IU-TC0755ut GB-speckles and GB-speckles, generated for the same nucleotide sequence with a single mutation (deletion). Subarea size for s-LASCA imaging is 7 x 7 pixels.

54 Subarea size for s-LASCA imaging is 10 x 10 pixels.
s-LASCA image for interfering of the omp1 E/IU-TC0755ut GB-speckles and GB-speckles, generated for the same nucleotide sequence with a single mutation (deletion). Subarea size for s-LASCA imaging is 10 x 10 pixels.

55 Subarea size for s-LASCA imaging is 15 x 15 pixels.
s-LASCA image for interfering of the omp1 E/IU-TC0755ut GB-speckles and GB-speckles, generated for the same nucleotide sequence with a single mutation (deletion). Subarea size for s-LASCA imaging is 15 x 15 pixels.

56 Summary GB-speckle, processed using s-LASCA technique, becomes more informative. s-LASCA images contains a lot of minutia, positions of these peculiarities depend on the number of mutations and their positions in the initial nucleotide sequences. s-LASCA images of interfering GB-speckles are more informative then bare GB-speckles, processed using s-LASCA technique.

57 ACKNOWLEDGEMENT This research has been supported by Russian Science Foundation, grant #

58 THANK YOU FOR ATTENTION!

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