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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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

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

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.

Nucleotide sequence omp1 for E/Bour(E1) ATGAAAAAACTCTTGAAATCGGTATTAGTATTTGCCGCTTTGAGTTCTGCTTCCTCCTTGCAAGCTCTGCCTGTGGGGAATCCTGCTGAACCAAGCCTTATGATCGACGGAATTCTGTGGGAAGGTTTCGGCGGAGATCCTTGCGATCCTTGCACCACTTGGTGTGACGCTATCAGCATGCGTATGGGTTACTATGGTGACTTTGTTTTCGACCGTGTTTTGAAAACAGATGTGAATAAAGAATTCCAAATGGGTGACAAGCCTACAAGTACTACAGGCAATGCTACAGCTCCAACCACTCTTACAGCAAGAGAGAATCCTGCTTACGGCCGACATATGCAGGATGCTGAGATGTTTACAAATGCCGCTTGCATGGCATTGAATATTTGGGATCGCTTTGATGTATTCTGTACACTAGGAGCCTCTAGCGGATACCTTAAAGGAAACTCTGCTTCTTTCAATTTAGTTGGATTGTTTGGAGATAATGAAAATCAAAGCACGGTCAAAACGAATTCTGTACCAAATATGAGCTTAGATCAATCTGTTGTTGAACTTTACACAGATACTGCCTTCTCTTGGAGCGTGGGCGCTCGAGCAGCTTTGTGGGAGTGCGGATGTGCGACTTTAGGGGCTTCTTTCCAATACGCTCAATCTAAACCTAAAGTCGAAGAATTAAACGTTCTCTGTAACGCAGCTGAGTTTACTATCAATAAGCCTAAAGGATATGTAGGGCAAGAATTCCCTCTTGCACTCATAGCAGGAACTGATGCAGCGACGGGCACTAAAGATGCCTCTATTGATTACCATGAGTGGCAAGCAAGTTTAGCTCTCTCTTACAGATTGAATATGTTCACTCCCTACATTGGAGTTAAATGGTCTCGAGCAAGTTTTGATGCCGATACGATTCGTATAGCCCAGCCAAAATCAGCTACAGCTATCTTTGATACTACCACGCTTAACCCAACTATTGCTGGAGCTGGCGATGTGAAAGCTAGCGCAGAGGGTCAGCTCGGAGATACCATGCAAATCGTCTCCTTGCAATTGAACAAGATGAAATCTAGAAAATCTTGCGGTATTGCAGTAGGAACGACTATTGTAGATGCAGACAAATACGCAGTTACAGTTGAGACTCGCTTGATCGATGAGAGAGCTGCTCACGTAAATGCACAATTCCGCTTCTAA

Nucleotide sequence omp1 for E/IU-TC0755ut ATGAAAAAACTCTTGAAATCGGTATTAGTATTTGCCGCTTTGAGTTCTGCTTCCTCCTTGCAAGCTCTGCCTGTGGGGAATCCTGCTGAACCAAGCCTTATGATCGACGGAATTCTGTGGGAAGGTTTCGGCGGAGATCCTTGCGATCCTTGCACCACTTGGTGTGACGCTATCAGCATGCGTATGGGTTACTATGGTGACTTTGTTTTCGACCGTGTTTTGAAAACAGATGTGAATAAAGAATTCCAAATGGGTGACAAGCCTACAAGTACTACAGGCAATGCTACAGCTCCAACCACTCTTACAGCAAGAGAGAATCCTGCTTACGGCCGACATATGCAGGATGCTGAGATGTTTACAAATGCCGCTTGCATGGCATTGAATATTTGGGATCGCTTTGATGTATTCTGTACACTAGGAGCCTCTAGCGGATACCTTAAAGGAAACTCTGCTTCTTTCAATTTAGTTGGATTGTTTGGAGATAATGAAAATCAAAGCACGGTCAAAACGAATTCTGTACCAAATATGAGCTTAGATCAATCTGTTGTTGAACTTTACACAGATACTGCCTTCTCTTGGAGCGTGGGCGCTCGAGCAGCTTTGTGGGAGTGCGGATGTGCGACTTTAGGGGCTTCTTTCCAATACGCTCAATCTAAACCTAAAGTCGAAGAATTAAACGTTCTCTGTAACGCAGCTGAGTTTACTATCAATAAGCCTAAAGGATATGTAGGGCAAGAATTCCCTCTTGCACTCATAGCAGGAACTGATGCAGCGACGGGCACTAAAGATGCCTCTATTGATTACCATGAGTGGCAAGCAAGTTTAGCTCTCTCTTACAGATTGAATATGTTCACTCCCTACATTGGAGTTAAATGGTCTCGAGCAAGTTTTGATGCCGATACGATTCGTATAGCCCAGCCAAAATCAGCTACAGCTATCTTTGATACTACCACGCTTAACCCAACTATTGCTGGAGCTGGCGATGTGAAAGCTAGCACAGAGGGTCAGCTCGGAGATACCATGCAAATCGTCTCCTTGCAATTGAACAAGATGAAATCTAGAAAATCTTGCGGTATTGCAGTAGGAACGACTATTGTAGATGCAGACAAATACGCAGTTACAGTTGAGACTCGCTTGATCGATGAGAGAGCTGCTCACGTAAATGCACAATTCCGCTTCTAA

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

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. 10336, 103360D-1-9, (2017)

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

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

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

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

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

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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

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

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

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.

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.

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.

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.

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.

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

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

ACKNOWLEDGEMENT This research has been supported by Russian Science Foundation, grant # 17-16-01099

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