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gFACs: Filtering, analysis, and conversion to unify genome annotations across alignment and gene prediction frameworks [article]

Madison Caballero, Jill Wegrzyn
2018 bioRxiv   pre-print
Summary: To provide oversight to the increasing number of published genome annotations, we present gFACs as a software package to filter, analyze, and convert predicted gene models and alignments. gFACs  ...  operates across a wide range of alignment, analysis, and gene prediction software inputs with a flexible framework for defining gene models with reliable structural and functional attributes. gFACs supports  ...  We also thank the members of the Plant Computational Genomics lab at the University of Connecticut: Sumaira Zaman, Nasim Rahmatpour, Taylor Falk, and Alex Trouern-Trend for the input on the software.  ... 
doi:10.1101/402396 fatcat:7has5qdxxrbf3eeimfyrswmmrm

gFACs: Gene Filtering, Analysis, and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks

Madison Caballero, Jill Wegrzyn
2019 Genomics, Proteomics & Bioinformatics  
To provide oversight to the increasing number of published genome annotations, we present a software package, the Gene Filtering, Analysis, and Conversion (gFACs), to filter, analyze, and convert predicted  ...  The software operates across a wide range of alignment, analysis, and gene prediction files with a flexible framework for defining gene models with reliable structural and functional attributes. gFACs  ...  Acknowledgments Supplementary material Supplementary data to this article can be found online at https://doi.org/10.1016/j.gpb.2019.04.002.  ... 
doi:10.1016/j.gpb.2019.04.002 pmid:31437583 pmcid:PMC6818179 fatcat:5dxv64sepnhovdiamdss6ve6gq

De novo genome assembly of the marine teleost, Bluefin Trevally (Caranx melampygus)

Brandon D Pickett, Jessica R Glass, Perry G Ridge, John S K Kauwe
2021 G3: Genes, Genomes, Genetics  
The assembly was annotated with 33.1K protein-coding genes, 71.4% of which were assigned putative functions, using RNA-seq data from eight tissues from the same individual.  ...  Most research to-date has been performed in Hawai'i, raising questions about the status of bluefin trevally populations across its Indo-Pacific range.  ...  ., and J. Wegrzyn, 2019 gFACs: Gene Filtering, Analysis, and Conversion to Unify 381 Genome Annotations Across Alignment and Gene Prediction Frameworks.  ... 
doi:10.1093/g3journal/jkab229 pmid:34568914 pmcid:PMC8473972 fatcat:jluqqph5sjcjbn76dkficqkp7m