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By a News Reporter-Staff News Editor at Life Science Weekly -- A new study on Life Science Research is now available. According to news reporting originating in Bethesda, Maryland, by NewsRx journalists, research stated, "Advances in high-throughput sequencing technology have yielded a large number of publicly available vertebrate genomes, many of which are selected for inclusion in NCBI's RefSeq project and subsequently processed by NCBI's eukaryotic annotation pipeline. Genome annotation results are affected by differences in available support evidence and may be impacted by annotation pipeline software changes over time."
The news reporters obtained a quote from the research from National Center for Biotechnology Information, "The RefSeq project has not previously assessed annotation trends across organisms or over time. To address this deficiency, we have developed a comparative protocol which integrates analysis of annotated protein-coding regions across a data set of vertebrate orthologs in genomic sequence coordinates, protein sequences, and protein features. We assessed an ortholog dataset that includes 34 annotated vertebrate RefSeq genomes including human. We confirm that RefSeq protein-coding gene annotations in mammals exhibit considerable similarity. Over 50% of the orthologous protein-coding genes in 20 organisms are supported at the level of splicing conservation with at least three selected reference genomes. Approximately 7,500 ortholog sets include at least half of the analyzed organisms, show highly similar sequence and conserved splicing, and may serve as a minimal set of mammalian 'core proteins' for initial assessment of new mammalian genomes. Additionally, 80% of the proteins analyzed pass a suite of tests to detect proteins that lack splicing conservation and have unusual sequence or domain annotation. We use these tests to define an annotation quality metric that is based directly on the annotated proteins thus operates independently of other quality metrics such as availability of transcripts or assembly quality measures. Results are available on the RefSeq FTP site [http://ftp.ncbi.nlm.nih.gov/refseq/supplemental/ProtCore/SM1.txt]. Our multi-factored analysis demonstrates a high level of consistency in RefSeq protein representation among vertebrates. We find that the majority of the RefSeq vertebrate proteins for which we have calculated orthology are good as measured by these metrics."
According to the news reporters, the research concluded: "The process flow described provides specific information on the scope and degree of conservation for the analyzed protein sequences and annotations and will be used to enrich the quality of RefSeq records by identifying targets for further improvement in the computational annotation pipeline, and by flagging specific genes for manual curation."
For more information on this research see: Comparison of RefSeq protein-coding regions in human and vertebrate genomes. Bmc Genomics, 2013;14():654. (BioMed Central - www.biomedcentral.com/; Bmc Genomics - www.biomedcentral.com/bmcgenomics/)
Our news correspondents report that additional information may be obtained by contacting J.H. Fong, National Center for Biotechnology Information, US, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, United States. Additional authors for this research include T.D. Murphy and K.D Pruitt (see also Life Science Research).
Keywords for this news article include: Bethesda, Maryland, Peptides, Proteins, Amino Acids, United States, Life Science Research, North and Central America.
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