Biology subjects

Gilbert, D. G.

Publications and source records attributed to Gilbert, D. G..

3 recordsLinked to original sources

bioRxiv2022

Genes ruler for genomes, Gnodes, measures assembly accuracy in animals and plants

Gnodes is a Genome Depth Estimator for animal and plant genomes, also a genome size estimator. It calculates genome sizes based on DNA coverage of assemblies, using unique, conserved gene spans for its standard depth. Results of this tool match the independent measures from flow cytometry of genome size quite well in tests with plants and animals. Tests on a range of model and non-model animal and plant genome assemblies give reliable and accurate results, in contrast to less reliable K-mer histogram methods. The problem of half-sized assemblies of duplication-rich Daphnia is addressed. A 20-year old Arabidopsis genome discrepancy is resolved in favor of 157Mb as measured with flow-cytometry. Not all genome DNA samples contain a genome, examples and reasons for this are discussed. The T2T completed human genome assembly of 2022 is complete by Gnodes measures, with about 5% uncertainty. With full genome DNA, Gnodes measures within 10%, usually within 5%, of flow cytometry, indicating they are both measuring the same content. Public URL: http://eugenes.org/EvidentialGene/other/gnodes/

bioinformatics↗

bioRxiv2019

Longest protein, longest transcript or most expression, for accurate gene reconstruction of transcriptomes?

Methods of transcript assembly and reduction filters are compared for recovery of reference gene sets of human, pig and plant, including longest coding sequence with EvidentialGene, longest transcript with CD-HIT, and most RNA-seq with TransRate. EvidentialGene methods are the most accurate in recovering reference genes, and maintain accuracy for alternate transcripts and paralogs. In comparison, filtering large over-assemblies by longest RNA measures, and most RNA-seq expression measures, discards a large portion of accurate models, especially alternates and paralogs. Accuracy of protein calculations is compared, with errors found in popular methods, as is accuracy of transcript assemblers. Gene reconstruction accuracy depends upon the underlying measurements, where protein criteria, including homology among species, have the strength of evolutionary biology that other criteria lack. EvidentialGene provides a gene reconstruction algorithm that is consistent with genome biology.

bioinformatics↗

bioRxiv2018

Genes of the Pig, Sus scrofa, reconstructed with Evidential Gene

The pig is a well-studied model animal of biomedical and agricultural importance. Genes of this species, Sus scrofa, are known from experiments and predictions, and collected at the NCBI Reference Sequence database section. Gene reconstruction from transcribed gene evidence of RNA-seq now can accurately and completely reproduce the biological gene sets of animals and plants. Such a gene set for the pig is reported here, including human orthologs missing from current NCBI and Ensembl reference pig gene sets, additional alternate transcripts, and other improvements. Methodology for accurate and complete gene set reconstruction from RNA is used: the automated SRA2Genes pipeline of EvidentialGene project.

genomics↗