A Shuffle-Based Statistical Approach for Robust Pseudogene Annotation

• Pedro M. Barcelos Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio)
• Marcos Catanho Fundação Oswaldo Cruz (Fiocruz)
• Antônio B. de Miranda Fundação Oswaldo Cruz (Fiocruz)
• Edward H. Haeusler Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio)
• Sérgio Lifschitz Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio)

DOI: https://doi.org/10.5753/bsb.2025.15172

Resumo

The accurate annotation of pseudogenes is a significant challenge in genomics, as their decaying sequences often fall into a "twilight zone" of similarity that confounds automated methods. This paper describes a robust, homology-based methodology designed to overcome this issue. The core of the approach is a shuffle-based statistical evaluation used to establish a custom, empirically-derived significance threshold. This allows for the confident discrimination of true, biologically significant sequence remnants from stochastic background noise, providing a reliable framework for annotating pseudogenes and unannotated coding sequences in large-scale genomic projects.

Palavras-chave: Pseudogene Annotation

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