Walsh code based numerical mapping method for the identification of protein coding regions in eukaryotes

Mechanical property is one of the most important properties of nanofiber membranes. Electrospinning is widely used in the preparation of nanofibers due to its advantages such as good stability and easy operation. Compared with some nature silk, the mechanical properties of nanofibers prepared by electrospinning are poor. Based on the principle of vortex spinning and DNA structure, this paper designed an air vortex electrospinning device that can control the structure of macromolecular chains in nanofibers. When a weak air vortex is generated in the electrospinning process, the macromolecule chains will entangle with each other and form a DNA-like structure so as to improve the mechanical property. In addition, when a strong air vortex is generated during the electrospinning process, the nanofibers will adhere to each other, thereby enhancing the mechanical property and enlarging the pore size.

Control of Macromolecule Chains Structure in a Nanofiber.

Based on the Chaos Game Representation(CGR) of DNA sequences,a novel 3D graphical representation of protein sequences is introduced in this paper.The x-,y-coordinates are the same to Randic's method,and the z-coordinate is the number of the amino acids in the sequence.The graphical representation has better visibility than the Randic's graphical representation.Furthermore,the graphical representation curve is characterized by two different mathematical methods.In addition,the similarity analysis based on the mathematical descriptors of protein sequences is given for the ND5 protein sequences of nine species.

A Graphical Representation of Protein Sequences and Its Applications

A new graph-theoretic approach to determine the similarity of genome sequences based on nucleotide triplets.

• CGR representation of SARS-CoV, SARS-CoV2, MERS and Alpha CoV sequences. • A combine performance of CGR and ANN to detect the virus sequences. • Encoding the genome sequence into an organized, well represented small data. • CGR transforms the genome sequence into short even less than 1% of actual size. In this study, chaos game representation (CGR) is introduced for investigating the pattern of genome sequences. It is an image representation of the genome for the overall visualization of the sequence. The CGR representation is a mapping technique that assigns each sequence base into the respective position in the two-dimension plane to portray the DNA sequence. Importantly, CGR provides one to one mapping to nucleotides as well as sequence. A coordinate of the CGR plane can tell the corresponding base and its location in the original genome. Therefore, the whole nucleotide sequence (until the current nucleotide) can be restored from the one point of the CGR. In this study, CGR coupled with artificial neural network (ANN) is introduced as a new way to represent the genome and to classify intra-coronavirus sequences. A hierarchy clustering study is done to validate the approach and found to be more than 90% accurate while comparing the result with the phylogenetic tree of the corresponding genomes. Interestingly, the method makes the genome sequence significantly shorter (more than 99% compressed) saving the data space while preserving the genome features. 

https://doi.org/10.1016/j.eswa.2022.116559

Detection of intra-family coronavirus genome sequences through graphical representation and artificial neural network

One novel representation of DNA sequence combining the global and local position information of the original sequence has been proposed to distinguish the different species. First, for the sufficient exploitation of global information, one graphical representation of DNA sequence has been formulated according to the curve of Fermat spiral. Then, for the consideration of local characteristics of DNA sequence, attaching each point in the curve of Fermat spiral with the related mass has been applied based on the relationships of neighboring four nucleotides. In this paper, the normalized moments of inertia of the curve of Fermat spiral which composed by the points with mass has been calculated as the numerical description of the corresponding DNA sequence on the first exons of beta-global genes. Choosing the Euclidean distance as the measurement of the numerical descriptions, the similarity between species has shown the performance of proposed method.

/pdf/one-novel-representation-of-dna-sequence-based-on-the-global-1sjj22q4mb.pdf

One novel representation of DNA sequence based on the global and local position information.

Abstract Background Therapeutic studies against human immunodeficiency virus type 1 (HIV-1) infection have become one of the important works in global public health. Methods Differential expression analysis was performed between HIV-positive (HIV+) and HIV-negative (HIV-) patients for GPL6947 and GPL10558 of GSE29429. Coexpression analysis of common genes with the same direction of differential expression identified modules. Module genes were subjected to enrichment analysis, Short Time-series Expression Miner (STEM) analysis, and PPI network analysis. The top 100 most connected genes in the PPI network were screened to construct the LASSO model, and AUC values were calculated to identify the key genes. Methylation modification of key genes were identified by the chAMP package. Differences in immune cell infiltration between HIV + and HIV- patients, as well as between antiretroviral therapy (ART) and HIV + patients, were calculated using ssGSEA. Results We obtained 3610 common genes, clustered into nine coexpression modules. Module genes were significantly enriched in interferon signalling, helper T-cell immunity, and HIF-1-signalling pathways. We screened out module genes with gradual changes in expression with increasing time from HIV enrolment using STEM software. We identified 12 significant genes through LASSO regression analysis, especially proteasome 20S subunit beta 8 (PSMB8) and interferon alpha inducible protein 27 (IFI27). The expression of PSMB8 and IFI27 were then detected by quantitative real-time PCR. Interestingly, IFI27 was also a persistently dysregulated gene identified by STEM. In addition, 10 of the key genes were identified to be modified by methylation. The significantly infiltrated immune cells in HIV + patients were restored after ART, and IFI27 was significantly associated with immune cells. Conclusion The above results provided potential target genes for early diagnosis and treatment of HIV + patients. IFI27 may be associated with the progression of HIV infection and may be a powerful target for immunotherapy.

https://www.tandfonline.com/doi/pdf/10.1080/07853890.2021.1995624?needAccess=true

Zhiyi Mo

Papers

One novel representation of DNA sequence based on the global and local position information.

IFI27 is a potential therapeutic target for HIV infection