Genewise

Genewise is a bioinformatics software tool used to predict gene structures by aligning protein sequences to genomic DNA. It is part of the Wise family of tools developed for genome annotation and comparative gene finding. Genewise combines amino acid-level similarity with models of intron-exon structure to infer the arrangement of exons, introns, and splice sites, producing a predicted coding sequence and its corresponding protein translation.

The program accepts a known protein sequence and a genomic DNA sequence and outputs a gene model that includes exon and intron coordinates, the predicted coding sequence, and the resulting protein. It is designed to handle complexities such as intron boundaries, frameshifts, sequencing errors, and small insertions or deletions, making it useful for annotating genes in newly sequenced genomes or for refining existing annotations.

Genewise has been widely used in genome annotation pipelines and comparative genomics studies. Its probabilistic modeling and integration of protein-level information with genomic context aimed to improve annotation accuracy beyond simple sequence alignments. Over time, Genewise influenced the development of subsequent protein-to-genome alignment tools and contributed to workflows that rely on cross-species similarity to identify and validate gene structures.

In the broader context of gene prediction, Genewise is often referenced alongside other alignment- and model-based approaches that link proteomes to genomes, illustrating the evolution of computational methods for annotating gene architectures in complex genomes.

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