https://scialert.net Trends in Bioinformatics en-us Science Alert Wed, 10 Jun 2026 18:11:57 +0200 Wed, 10 Jun 2026 18:14:14 +0200 RssPublisher 0.2.0 beta https://scialert.net/images/logo.gif https://scialert.net 41 233 Trends in Bioinformatics Transcriptional Patterns of High-Risk Human Papillomavirus Types 16, 18, 45, 68b Genes Background and Objective: Persistent high-risk human papillomavirus (HR-HPV) infections together with their oncogene expressions are necessary for cervical cancer development. We aimed to detect transcription patterns and the major viral oncogene transcripts expressed in five cervical cancer cell lines containing integration form of four HR-HPV types 16, 18, 45 and 68b. Materials and Methods: RNA extracted from five cervical cancer cell lines (CaSki, SiHa, HeLa, MS751 and ME180) were used for RNA sequencing analysis on an Illumina HiSeq2500. The HISAT2, Cufflinks, Cuffmerge and Cuffdiff were used to analyze the data. The HPV transcripts were quantified as fragments per kilobase per million (FPKM). Real-time PCR was performed to validate and differential viral gene expressions. Results: The major and common transcripts obtained from four HR-HPV types 16, 18, 45 and 68b were E6*I with splicing event occur within the E6 gene fused with full-length E7 ORF, 226^409 (HPV16), 233^416 (HPV18), 230^412 (HPV45) and 129^311(HPV68b) and were associated with full-length E7 oncogene expression. Real-time PCR revealed that full-length HR-HPV E7 oncogene was highly expressed in all five cell lines. Conclusion: Splicing patterns that occurred within the E6 gene resulting in the E6*I transcript facilitates E7 oncogene translation. Various transcripts obtained from four HR-HPV types are useful for further functional study of truncated viral proteins expressed from different HPV types.]]> https://scialert.net/abstract/?doi=tb.2021.1.12 10 June, 2026 Validation of Isolate Stability Status and in silico Characterization of SARS-COV 2 Partial CdsRdRP Gene Sequences Background and Objective: In December 2019, patients diagnosed with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (COVID 19). The article aimed to unmask the genetic stability and nature of the viruses and validated the safety guidelines adopted for the coronaviruses currently causing the global pandemic. Materials and Methods: This study uses in silico approach and bioinformatics tools to validate the stability status and characteristics of the novel SARS-COV 2 coronaviruses by retrieving nucleotide sequences isolated and deposited in the NCBI. Results: The results have revealed that 11 out of 12 isolates studied are genetically and thermally unstable. The aliphatic index ranged from 52.98-112.07 in MT187977.1-MT127116.1, respectively. The instability index among the sequences ranged from 39.58-73.65 in MT187977.1-MT152900.1 isolate, respectively. The G-C contents range from 37.28-49.26% in MN938385.1-MT187977.1, respectively. Phylogenetically, isolates MT127116.1, MT159778.1, MT050414.1 and MT042777.1 showed the same genetic and mutation pathway with an evolutionary distance of 0.4 and 0.8 divergence times relative to the last common ancestor. Conclusion: There is a need for concerted effort in studying and understanding the genetic and thermal stability status and other characteristics of the viruses to be able to find a suitable therapy and drug design for the pandemic and biosecurity of humans against the virus now and in the future.]]> https://scialert.net/abstract/?doi=tb.2021.13.27 10 June, 2026