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Updated: Jun 30, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
Published on: December 22, 2017
A new approach for gene annotation using unambiguous sequence joining
Alexandre Tchourbanov1, Daniel Quest, Hesham Ali
1Department of Computer Science, University of Nebraska at Omaha, 68182-0116, USA. achurbanov@mail.unomaha.edu
Abstract:
The problem addressed by this paper is accurate and automatic gene annotation following precise identification/ annotation of exon and intron boundaries of biologically verified nucleotide sequences using the alignment of human genomic DNA to curated mRNA transcripts. We provide a detailed description of a new cDNA/DNA homology gene annotation algorithm that combines the results of BLASTN searches and spliced alignments. Compared to other programs currently in use, annotation quality is significantly increased through the unambiguous junction of genomic DNA sequences. We also address gene annotation with both non-canonic splice sites and short exons. The approach has been tested on the Genie learning subset as well as full-scale human RefSeq, and has demonstrated performance as high as 97%.
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