FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2028195030> ?p ?o ?g. }

• W2028195030 abstract "To the Editor: We are also concerned about errors in GenBank sequences, and that is why we took precautions to evaluate the effects of potential sequence errors.1xThe Diversity Present in 5140 Human Mitochondrial Genomes. Pereira, L., Freitas, F., Fernandes, V., Pereira, J.B., Costa, M.D., Costa, S., Maximo, V., Macaulay, V., Rocha, R., and Samuels, D.C. Am. J. Hum. Genet. 2009; 84: 628–640Abstract | Full Text | Full Text PDF | PubMed | Scopus (77)See all References1 But many of the potential errors reported by Yao et al. are highly subjective. They defined “phantom mutations” as (with exceptions) the exclusive presence of rare transversions in a specific data set. Although it is reasonable to be skeptical of such variations, surely such rare variations do actually occur without being errors. To deal with potential sequence errors, we took the step of doing the analysis twice; once for all reported variations and once for only variations present in more than 0.1% of the sequences. We made the latter choice to filter out sequencing errors, assuming that specific errors would not be repeated in many different sequences. This filtering process did remove 94% of their listed “phantom mutations.” As Yao et al. acknowledge, the removal of these rare variations (some of which may be sequencing errors) had little effect on most of our results.Yao et al. define “missing variants” as those variants expected to be seen in a particular haplogroup but not reported in a sequence assigned to it. The problem with this definition is that it presupposes that we already have a complete picture of mtDNA variation and that all deviations from it are errors. There are many examples of such “missing variants” being true variations. It was once thought that all L- sub-Saharan haplogroups had the substitution at position 16223, but later some lineages were characterized without it (L0d1a, L1c1a1, L2d, L3x2a). Also, the M1- defining substitution at position 16249 is absent in the branch M1a1a.After the careful data mining of Yao et al., potential errors were found in < 200 of the 5140 sequences. So, ∼96% of the sequences deposited in GenBank by the end of August 2008 did pass their extreme quality filter. Yao et al. list many cases in which errors in the original sequences have been acknowledged and corrected by authors but the GenBank sequence has not been updated. GenBank2xGenBank. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Sayers, E.W. Nucleic Acids Res. 2009; 37: D26–D31Crossref | PubMed | Scopus (390)See all References2 allows the sequence depositor to update that sequence, but it depends on each depositor to carry out this procedure. Identifying these possible sequence errors is complex and is arguably highly subjective. To expect every author of a sequence data-mining project to carry out such a very subjective quality-control step is not reasonable, in our opinion.Though we may disagree on specifics raised by Yao et al., we do share with them a concern about mtDNA sequence quality. Spirited discussions such as this one have been going on for the past decade. It is time to provide the mtDNA research community with analysis tools that allow them to efficiently check their sequences for potential problems, such as sequencing errors or unusual variations. We tried to go forward in this direction with our paper1xThe Diversity Present in 5140 Human Mitochondrial Genomes. Pereira, L., Freitas, F., Fernandes, V., Pereira, J.B., Costa, M.D., Costa, S., Maximo, V., Macaulay, V., Rocha, R., and Samuels, D.C. Am. J. Hum. Genet. 2009; 84: 628–640Abstract | Full Text | Full Text PDF | PubMed | Scopus (77)See all References1 by providing the mtDNA Gene-Syn software. Fortunately, others are also advancing along the same path.3xMITOMASTER: A Bioinformatics Tool for the Analysis of Mitochondrial DNA Sequences. Brandon, M.C., Ruiz-Pesini, E., Mishmar, D., Procaccio, V., Lott, M.T., Nguyen, K.C., Spolim, S., Patil, U., Baldi, P., and Wallace, D.C. Hum. Mutat. 2009; 30: 1–6Crossref | PubMed | Scopus (25)See all References, 4xUpdated comprehensive phylogenetic tree of global human mitochondrial DNA variation. van Oven, M. and Kayser, M. Hum. Mutat. 2009; 30: E386–E394Crossref | PubMed | Scopus (625)See all References, 5xmtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences. Lee, H.Y., Song, I., Ha, E., Cho, S.B., Yang, W.I., and Shin, K.J. BMC Bioinformatics. 2008; 9: 483Crossref | PubMed | Scopus (2)See all References" @default.
• W2028195030 created "2016-06-24" @default.
• W2028195030 creator A5009870321 @default.
• W2028195030 creator A5043999573 @default.
• W2028195030 date "2009-12-01" @default.
• W2028195030 modified "2023-09-28" @default.
• W2028195030 title "Response to Yao et al." @default.
• W2028195030 cites W1965330509 @default.
• W2028195030 cites W1969804739 @default.
• W2028195030 cites W2068895135 @default.
• W2028195030 cites W2111668248 @default.
• W2028195030 doi "https://doi.org/10.1016/j.ajhg.2009.10.022" @default.
• W2028195030 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2790563" @default.
• W2028195030 hasPublicationYear "2009" @default.
• W2028195030 type Work @default.
• W2028195030 sameAs 2028195030 @default.
• W2028195030 citedByCount "1" @default.
• W2028195030 countsByYear W20281950302012 @default.
• W2028195030 crossrefType "journal-article" @default.
• W2028195030 hasAuthorship W2028195030A5009870321 @default.
• W2028195030 hasAuthorship W2028195030A5043999573 @default.
• W2028195030 hasBestOaLocation W20281950301 @default.
• W2028195030 hasConcept C104317684 @default.
• W2028195030 hasConcept C151994961 @default.
• W2028195030 hasConcept C180754005 @default.
• W2028195030 hasConcept C197754878 @default.
• W2028195030 hasConcept C201526758 @default.
• W2028195030 hasConcept C23161992 @default.
• W2028195030 hasConcept C24586158 @default.
• W2028195030 hasConcept C2778112365 @default.
• W2028195030 hasConcept C52119013 @default.
• W2028195030 hasConcept C54355233 @default.
• W2028195030 hasConcept C554144382 @default.
• W2028195030 hasConcept C70721500 @default.
• W2028195030 hasConcept C78458016 @default.
• W2028195030 hasConcept C79029880 @default.
• W2028195030 hasConcept C86803240 @default.
• W2028195030 hasConcept C95457728 @default.
• W2028195030 hasConceptScore W2028195030C104317684 @default.
• W2028195030 hasConceptScore W2028195030C151994961 @default.
• W2028195030 hasConceptScore W2028195030C180754005 @default.
• W2028195030 hasConceptScore W2028195030C197754878 @default.
• W2028195030 hasConceptScore W2028195030C201526758 @default.
• W2028195030 hasConceptScore W2028195030C23161992 @default.
• W2028195030 hasConceptScore W2028195030C24586158 @default.
• W2028195030 hasConceptScore W2028195030C2778112365 @default.
• W2028195030 hasConceptScore W2028195030C52119013 @default.
• W2028195030 hasConceptScore W2028195030C54355233 @default.
• W2028195030 hasConceptScore W2028195030C554144382 @default.
• W2028195030 hasConceptScore W2028195030C70721500 @default.
• W2028195030 hasConceptScore W2028195030C78458016 @default.
• W2028195030 hasConceptScore W2028195030C79029880 @default.
• W2028195030 hasConceptScore W2028195030C86803240 @default.
• W2028195030 hasConceptScore W2028195030C95457728 @default.
• W2028195030 hasLocation W20281950301 @default.
• W2028195030 hasLocation W20281950302 @default.
• W2028195030 hasLocation W20281950303 @default.
• W2028195030 hasOpenAccess W2028195030 @default.
• W2028195030 hasPrimaryLocation W20281950301 @default.
• W2028195030 hasRelatedWork W1986995088 @default.
• W2028195030 hasRelatedWork W1990123660 @default.
• W2028195030 hasRelatedWork W1992629151 @default.
• W2028195030 hasRelatedWork W1994790031 @default.
• W2028195030 hasRelatedWork W1997298837 @default.
• W2028195030 hasRelatedWork W1999581988 @default.
• W2028195030 hasRelatedWork W2028778576 @default.
• W2028195030 hasRelatedWork W2029793306 @default.
• W2028195030 hasRelatedWork W2032202794 @default.
• W2028195030 hasRelatedWork W2055135367 @default.
• W2028195030 hasRelatedWork W2060468715 @default.
• W2028195030 hasRelatedWork W2062060849 @default.
• W2028195030 hasRelatedWork W2066530267 @default.
• W2028195030 hasRelatedWork W2070836068 @default.
• W2028195030 hasRelatedWork W2076058897 @default.
• W2028195030 hasRelatedWork W2095369010 @default.
• W2028195030 isParatext "false" @default.
• W2028195030 isRetracted "false" @default.
• W2028195030 magId "2028195030" @default.
• W2028195030 workType "article" @default.