SEQSIM - A novel bioinformatics tool for comparisons of upstream gene regions - a case study of calcium binding protein spermatid associated 1 (CABS1)

The regulation of gene expression is carefully overseen by upstream gene regions (UGRs) which include promoters, enhancers, and other regulatory elements. Understanding these regions is difficult using standard bioinformatic approaches due to the scale of the human genome. Here we present SEQSIM, a novel bioinformatics tool based on a modified Needleman-Wunsch algorithm that allows for fast, comprehensive, and accurate comparison of UGRs across the human genome. In this study, we detailed the applicability and validity of SEQSIM through an extensive case study of the calcium binding protein spermatid-associated 1 (CABS1). By analyzing 2000 base pairs upstream of every human gene, SEQSIM identified distinct clusters of UGRs, revealing conserved motifs and suggesting potential regulatory interactions. Our analysis identified 41 clusters, the second largest of which contains the CABS1 UGR. Studying the other members of the CABS1 cluster could offer new insights into its regulatory mechanisms and suggest broader implications for genes involved in similar pathways or functions. The development and implementation of SEQSIM represents a significant step forward for the genomics field, providing a powerful new tool to dissect the complexity of the human genome and gain a better understanding of how gene expression is regulated. The study not only shows that SEQSIM is an effective means to identify potential regulatory elements and gene clusters, but also opens up new lines of inquiry to understand overall genomic architecture.