Abstract
Selected abstracts of \u201cBioinformatics: from Algorithms to Applications 2020\u201d conference
Highlights
Transcription factor binding sites (TFBS or operators) are the most abundant regulatory elements in genomes
The contacts between operators and DNA-binding domains (CR-tag) based TFBS inference method is applicable to any bacterium and can find the majority of TFBSs in uncharacterised bacterial genomes
The proposed workflow might contribute as a state art methodology to design bioinformatics workflows for specific genus as well as contributing to the understanding of the role implied by commensal and clinical enterococci in different environments and to promote elucidation of biological mechanisms which made this bacterial genus associated with public health risks
Summary
Transcription factor binding sites (TFBS or operators) are the most abundant regulatory elements in genomes. Materials and methods The squalene synthase (SS) and SSL genes of the organism were sequenced using Illumina reads and SOAP and Velvet assembly, in such a way that the rest of the genome was essentially ignored but this gene family was retrieved in complete detail. By this means the full set of paralogues were determined. Results Our workflow uses information from multiple-Reference genomes to obtain an improved assembly of the simulated reads of Escherichia coli (NZ_CP027599.1). Conclusions A proof-of-concept using simulated short-read data sets of Escherichia coli is presented to highlight the improvements in the assembly guided by multiple Reference genomes
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