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Simplified search suggestions : Raja Farhana Raja Khairuddin

A computational approach to studying the evolution of streptococcal quorum sensing systems

Abstract

For many years, researchers have studied the social lives of bacteria to understand intra- and inter-species interactions. Cell-cell communication, also known as quorum sensing (QS), is used by bacteria to coordinate their behaviour in response to environmental conditions. The QS system in Streptococcus species is well known to regulate competence. Studies show that Streptococcus pneumoniae has two homologous QS systems: 1) the competence (Com) system that regulates competence; and 2) a bacteriocin-like peptide (Blp) system that regulates the production of bacteriocins. Both functions are widespread in the genus. In S. pneumoniae, the Blp QS system shares a common ancestor and has similar features to the Com QS system. However, the evolutionary relationship between these QS systems remains obscure. SUCRE methodology was developed to identify the QS homologous genes in the streptococcal species. SUCRE uses four complementary approaches: homology search, putative gene finding, regulon co.....

Thesis Published 2014 3258 hits Available

In silico identification of prospective virulence factors associated with candidiasis in Meyerozyma guilliermondii strain SO from genome dataset

Raja Farhana Raja Khairuddin

Abstract

Background: Meyerozyma guilliermondii is a prospective yeast that has extensively contributed to the biotechnology sector. In 2015, M. guilliermondii strain SO which was isolated from spoiled orange has successfully been developed as an inducer-free expression system and attained a significant impact in producing industrially important recombinant proteins. The species possesses high similarity to Candida albicans which may cause candidiasis. The industrial-benefiting M. guilliermondii strain SO has been underexplored for its virulence status. Thus, this study aimed to document the potential virulence factors through the comprehensive in silico analysis of M. guilliermondii strain SO genome. This analysis demonstrated the molecular characterization which could distinguish the pathogenicity status of M. guilliermondii. Results: The genome data were generated from Illumina HiSeq 4000 sequencing platform and assembled into 51 scaffolds successfully accumulating a genome size of 10.63 Mbp......

Article Published 2023 449 hits Available

Genome assembly composition of the string "ACGT" array: a review of data structure accuracy and performance challenges

Raja Farhana Raja Khairuddin

Abstract

Background. The development of sequencing technology increases the number of genomes being sequenced. However, obtaining a quality genome sequence remains a challenge in genome assembly by assembling a massive number of short strings (reads) with the presence of repetitive sequences (repeats). Computer algorithms for genome assembly construct the entire genome from reads in two approaches. The de novo approach concatenates the reads based on the exact match between their suffix-prefix (overlapping). Reference-guided approach orders the reads based on their offsets in a well-known reference genome (reads alignment). The presence of repeats extends the technical ambiguity, making the algorithm unable to distinguish the reads resulting in misassembly and affecting the assembly approach accuracy. On the other hand, the massive number of reads causes a big assembly performance challenge. Method. The repeat identification method was introduced for misassembly by prior identification of repet.....

Article Published 2023 591 hits Available

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