Search for gene sequence, RNA secondary structure and biochemical and taxonomic information about organelles. Lee YS, Oh J, Kim YU, Kim N, Yang S, Hwang UW: Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals. The SUI was developed using Ajax technology, which supports faster performance than other methods (e.g. Bioinformatics.
MitoFish and MitoAnnotator: a mitochondrial genome database of fish government site. Find information about the proteins involved in mitosis. 2007, 66 (2): 371-382. The mtDNA-encoded polypeptides are all subunits of enzyme complexes of the oxidative phosphorylation system. In addition, the interactive capability of graphical presentation of sequence alignments and selecting and storing all sequences under a selected node in the resulting phylogenetic tree by clicking the node is also provided.
MODB: a comprehensive mitochondrial genome database for Mollusca Here, we present AmtDB, the first database of ancient human mitochondrial genomes. doi: 10.1093/nar/gkh137. Feijao PC, Neiva LS, de Azeredo-Espin AM, Lessinger AC: AMiGA: the arthropodan mitochondrial genomes accessible database. FOIA The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Mitochondrial genomes of parasitic arthropods: implications for studies of population genetics and evolution. Med Vet Entomol. 10.1093/nar/22.22.4673. Instead, separate allele counts and frequencies are provided for both homoplasmic and heteroplasmic variants as well as for each top-level haplogroup. The .gov means its official. KJ designed the IMGD web site and developed SUI. Waeschenbach A, Telford MJ, Porter JS, Littlewood DT: The complete mitochondrial genome of Flustrellidra hispida and the phylogenetic position of Bryozoa among the Metazoa. 10.1006/mpev.1998.0580. All other annotations with LOFTEE remain unchanged, and caution should be taken to interpret the annotations in the context of the mitochondrial genome. 10.1073/pnas.0510466103. BLAST the Human Genome Microbial Nucleotide BLAST Genome Annotation and Analysis Eukaryotic Genome Annotation Prokaryotic Genome Annotation PASC (Pairwise Sequence Comparison) External Resources GOLD - Genomes Online Database Bacteria Genomes at Sanger Ensembl You are here: NCBI > Genomes & Maps > Genome Clipboard, Search History, and several other advanced features are temporarily unavailable. Sequencing, however, is not a skill that is part of the routine forensic analysis because of the relative rarity of requests, and . Daniel MacArthur, Monkol Lek, and Vamsi Mootha provided leadership and analytical advice. Search for information on eukaryotic proteins localized to organelles and subcellular structures. J.P. acknowledges a graduate fellowship provided by the Ministry of Education through the Brain Korea 21 Project. Human mitochondrial genetics is the study of the genetics of human mitochondrial DNA (the DNA contained in human mitochondria).The human mitochondrial genome is the entirety of hereditary information contained in human mitochondria.
We developed a mitochondria mode of GATK MuTect2 to call variants in GRCh38 chrM (identical to the revised Cambridge Reference Sequence, rCRS, GenBankNC_012920.1) on individual samples.
mtDB: Human Mitochondrial Genome Database, a resource for population PubMed 2008, 9 (1): 402-10.1186/1471-2164-9-402. Zootaxa. Epub 2022 Dec 15. We hope that the addition of mtDNA to gnomAD will enable researchers to better understand the role of mtDNA variation in both health and disease states. Truncated table of polymorphic sites. 1995, 376 (6536): 163-165. . sharing sensitive information, make sure youre on a federal Users can choose the number of mitochondrial genomes to be displayed by selecting them via SUI. To display different features on the genome graphically, the browser uses three different colors for PCGs, tRNAs, and rRNAs, and presents names of individual units (Figure 6). Poly, a human genome polymorphism database]. 1980;77:67156719. Mol Phylogenet Evol. Our mtDNA data include allele frequencies for heteroplasmic and homoplasmic variants, haplogroup-specific allele frequencies, predicted consequences for protein and tRNA variants, and links to mitochondrial resources. The SNP database incorporated to IMGD presents the distribution of SNPs and INDELs in the mitochondrial genomes of multiple isolates within eight species. Epub 2006 Oct 28. -, Holt I.J., Harding A.E., Petty R.K., Morgan-Hughes J.A. The probe was prepared by PCR amplification of total human DNA corresponding to positions 3305 and 12413 of the mitochondrial genome. The Species-driven User Interface (SUI) consists of three parts: i) Species search, ii) Taxon browser, and iii) Species cart. A new mitochondrial disease associated with mitochondrial DNA heteroplasmy. Low or high mtDNA copy number: Samples with an estimated mtDNA copy number less than 50 were removed (N=6,505 samples) since they are prone to contamination and NUMT-derived false positive calls. Boore JL, Brown WM: Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. The Taxon browser provides the interface for browsing taxa in a hierarchical manner. Yang Z: PAML 4: phylogenetic analysis by maximum likelihood. This database is dedicated to collecting, sorting and sharing basic information regarding mollusks, especially their mitochondrial genome information. The Mollusca mitochondrial database (MODB) was established for the Life and Health Big Data Center of Yantai University. The gene order browser implemented in IMGD was designed for efficient graphical presentation of PCGs, tRNAs, and rRNAs in the mitochondrial genome. Park et al., unpublished). Vertebrate MitBASE: a specialised database on vertebrate mitochondrial DNA sequences. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS).
MODB: a comprehensive mitochondrial genome database for Mollusca Rapid evolution of animal mitochondrial DNA. Among the 13 PCGs, the COI, NADH dehydrogenase subunit 4 (ND4), and/or NADH dehydrogenase subunit 5 (ND5) genes showed the highest frequency of SNPs in Diptera (COI and ND5) and Isoptera (cytochrome b, ND4, and ND5) (Figure 4). Would you like email updates of new search results? We developed IMGD to support versatile comparative analyses of hexapod mitochondrial gene/genome sequences. Epub 2006 Oct 11. Mitochondrial DNA is the small circular chromosome found inside mitochondria. Mitochondrial genes are highly polymorphic and cataloguing existing variation is of interest for medical scientists involved in the identification of mutations causing mitochondrial dysfunction, as well as for population genetics studies. Mitochondrial DNA Polymorphism in HV1 and HV2 Regions and 12S rDNA in Perimenopausal Hypertensive Women. For example, the AF_hom annotation provides the overall allele frequency taking into account only variants that were called homoplasmic in samples with that variant (heteroplasmy 95-100%). The closed red circle indicates the average GC content, and the blue and red bars present the maximum and minimum GC contents, respectively. In contrast, the following 13 orders (39.39%) are represented only by less than 50 species in total: Dermaptera, Siphonaptera, Zygentoma, Grylloblattodea, Mantophasmatodea, Embioptera, Diplura, Archaeognatha, Strepsiptera, Megaloptera, Raphidioptera, Protura, and Zoraptera (Table 1). The IMGD archives sequences and taxonomical information from more than 25,000 hexapod species. Examples of phylogenetic analyses conducted using data and tools in IMGD. SNPs in the cytochrome c oxidase subunits I (COI) locus of Aedes aegypti (Diptera: Cuclicidae) were used to differentiate four strains [14]. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. 2003 Dec;19(12):709-16. doi: 10.1016/j.tig.2003.10.012. Ptycta johnsoni (Psocoptera) was used as an outgroup. Pfenninger M, Nowak C, Kley C, Steinke D, Streit B: Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species. 2008, 36: D562-D571.
MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish Three different methods of drawing phylogenetic trees (NJ, MP, and ML) are currently available. Gene insertions and deletions were detected in Collembola, Ephemeroptera, Orthoptera, Hemiptera, Phthiraptera, Diptera, and Lepidoptera. The human reference genome assembly and sequence information that is represented in the RefSeq collection is identical to the sequence data available in databases maintained by the International Nucleotide Sequence Database Collaboration ( INSDC ) including NCBI's GenBank database. Four assemblies of the matsutake genome are currently available in a public DNA database. Proc Natl Acad Sci USA. Cookies policy. 2007, 7 (3): 355-364. Syst Entomol. Nick Watts adapted the gnomAD browser to incorporate mitochondria-specific annotations. The https:// ensures that you are connecting to the Database Curator ; Mitochondrial Mutations, MITOMAP : D.C.Wallace and Consortium Emory Univ. Search for comprehensive information on nuclear genes encoding proteins involved in mitochondrial biogenesis and function. Nicole Lake conducted analyses to aid in quality control. The SUI of IMGD supports efficient data retrieval and analysis at multi-taxon levels.
mtDB - Human Mitochondrial Genome Database PubMed The genome sizes vary from 12,984 bp to 19,517 bp, with an average of 15,617 bp with no clear correlation at any taxon levels (Figure 2B). 2001 Dec;18(6):482-5. AMPDB -- the Arabidopsis Mitochondrial Protein Database, ARWEN -- a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences, GOBASE -- A database of mitochondrial and chloroplast information, HMPD -- Human mitochondrial protein database, HvrBase++ -- a phylogenetic database for primate species, MAPU -- Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes, MITOMAP -- a human mitochondrial genome database, MiCroKit -- MIdbody, CentROsome and KIneTochore database, MitoDat - Mendelian Inheritance and the Mitochondrion, MitoDrome -- A database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion, MitoGenesisDB -- Mitochondrial Spatio-Temporal Expression Database, MitoP2 -- An Integrated Database on Mitochondrial Proteins in Yeast, Man, mouse, and Neurospora, MitoProteome -- Mitochondrial Protein Sequence Database and Annotation System, Mitome -- dynamic and interactive database for comparative mitochondrial genomics in metazoan animals, OGRe -- A relational database for comparative analysis of mitochondrial genomes, Organelle DB -- a cross-species database of protein localization and function, PeroxisomeDB -- a database for the peroxisomal proteome, functional genomics and disease, Yeast Deletion Project and Proteomics of Mitochondria Database, mtDB -- Human Mitochondrial Genome Database, a resource for population genetics and medical sciences, plprot -- a comprehensive proteome database for different plastid types, OBRC: Online Bioinformatics Resources Collection, DNA Sequence Databases and Analysis Tools, Gene Mutations, Genetic Variations and Diseases, Microarray, SAGE, and other Gene Expression, Other Databases and Tools (Literature Mining, Lab Protocols, Medical Topics, and others), Protein Sequence Databases and Analysis Tools. Coral genome sequence assemblies and gene catalogs. Part of Article Nelson LA, Wallman JF, Dowton M: Using COI barcodes to identify forensically and medically important blowflies. Bioinformatics. Science.
MitoZoa: A curated mitochondrial genome database of metazoans for Estimates of the GC content and genome size of the 132 hexapod mitochondrial genomes. 10.1038/33577. 2003, 31 (13): 3406-3415. BMC Genomics. Parasitology. Nucleic Acids Res. Morlais I, Severson DW: Complete mitochondrial DNA sequence and amino acid analysis of the cytochrome C oxidase subunit I (COI) from Aedes aegypti. Therefore to call control region variants, we extracted all chrM reads and realigned them to a mitochondrial reference that was shifted by 8,000 bases, called variants on this shifted alignment, and then converted coordinates back to their original positions. 10.1038/376163a0. Cameron SL, Lambkin CL, Barker SC, Whiting MF: A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbas e.pl. Privacy 2007 Jan;35(Database issue):D66-70. The MP trees based on the COI gene sequences (Figure 3B and 3C) revealed more comprehensive phylogenetic relationships than those derived from previous studies in the orders Phthiraptera [4244] and Mantophasmatodea [45, 46]. Mitochondrial DNA . Wonhoon Lee, Jongsun Park contributed equally to this work. 10.1016/j.ympev.2007.04.020. This will help users manage their own datasets via IMGD. Solignac M: Mitochondrial DNA in the Drosophila melanogaster complex. PMC. Park J, Park J, Jang S, Kim S, Kong S, Choi J, Ahn K, Kim J, Lee S, Kim S, Park B, Jung K, Kim S, Kang S, Lee YH: FTFD: An Informatics Pipeline Supporting Phylogenomic Analysis of Fungal Transcription Factors. Recent expansions in the capabilities of mtDB include a haplotype search function and the ability to identify and download sequences carrying particular variants. Disclaimer. -, Brown W.M., George M., Jr, Wilson A.C. The IMGD, supported by the SNP analysis platform and the SNU Genome Browser, provides a graphical view of mitochondrial genome comparisons.
Human mitochondrial genetics - Wikipedia Search for information on the predicted and experimentally confirmed protein complement of mitochondria from the model plant Arabidopsis thaliana. Kress WJ, Erickson DL: DNA barcodes: genes, genomics, and bioinformatics. 1997, 25 (5): 955-964. Nucleic Acids Res. Gene. Carone A, Malladi SB, Attimonelli M, Saccone C. Nucleic Acids Res. CAS 2022 Mar 17;4(1):13. doi: 10.1186/s42238-022-00123-2. Search for comprehensive genomic information on mitochondria and chloroplasts. The browser in Favorite provides four options: 'Edit,' 'Function,' 'Analysis,' and 'Download.' After placing the taxa of interest in the cart, they can be analyzed in the following ways: i) downloading nucleotide and protein sequences and/or storing them into the Favorite with various options, ii) comparing gene orders, GC content/AT skew, codon usage and position among mitochondrial genomes, iii) displaying tRNA secondary structures predicted by tRNAScan-SE [27] and mFold [28], iv) executing ClustalW for multiple sequence alignment and calculating phylogenetic trees based on three methods, including NJ, MP, and ML, with a bootstrapping option, v) executing a BLAST search against the selected taxa, and vi) saving species information into the Favorite for future analyses (Figure 5). Selective constraints and pathogenicity of mitochondrial DNA variants inferred from a novel database of 196,554 unrelated individuals, Bolze * and Mendez * et.
V-MitoSNP: visualization of human mitochondrial SNPs | BMC 10.1006/mpev.2001.1028. Nucleic Acids Res. Vasconcelos AT, Guimaraes AC, Castelletti CH, Caruso CS, Ribeiro C, Yokaichiya F, Armoa GR, Pereira Gda S, da Silva IT, Schrago CG, Fernandes AL, da Silveira AR, Carneiro AG, Carvalho BM, Viana CJ, Gramkow D, Lima FJ, Correa LG, Mudado Mde A, Nehab-Hess P, Souza R, Correa RL, Russo CA: MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies. -, Ingman M., Kaessmann H., Paabo S., Gyllensten U. Mitochondrial genome variation and the origin of modern humans. (A) Each rectangular box shows three layers. (B) MP tree built based on 88 COI sequences from 70 Phthirapteran species using DNAPARS, is shown. [Introduction to Go! 2004, 120 (13): 41-50. Unauthorized use of these marks is strictly prohibited. The Favorite is linked to CFGP (http://cfgp.snu.ac.kr/), which provides not only diverse bioinformatic tools but also a data warehouse containing complete sequences of 19 insect nuclear genomes [24], so that further analyses with diverse resources can be conducted easily via this web interface. 2004, 32: W20-25. In particular, members of Diptera and Coleoptera account for 26 (20.00%) and 12 (9.23%) mitochondrial genomes, respectively, reflecting active researches on these orders [39, 40]. A total of 856 SNPs and 30 insertion and deletions (INDELs) were identified (Table 4) from 187 kbp of aligned mitochondrial genome sequences (6 pair-wise comparisons of mitochondrial genomes). 1999, 11 (2): 283-287. Catalano D, Licciulli F, Turi A, Grillo G, Saccone C, D'Elia D. BMC Bioinformatics. In the first step, completely and partially sequenced mitochondrial genome sequences are downloaded from NCBI using proper keywords after filtering out unpublished sequences. Jung K, Park J, Choi J, Park B, Kim S, Ahn K, Choi J, Choi D, Kang S, Lee Y-H: SNUGB: a versatile genome browser supporting comparative and functional fungal genomics.
Mitochondrial DNA sequence variation and risk of glioma. PMC -. NUMTs: Nuclear sequences of mitochondrial origin (termed NUMTs) are derived from pieces of mtDNA that have integrated into the nuclear genome over the course of human evolution. Stahls G, Savolainen E: MtDNA COI barcodes reveal cryptic diversity in the Baetis vernus group (Ephemeroptera, Baetidae).
gnomAD v3.1 Mitochondrial DNA Variants | gnomAD browser - Broad Institute effusa genome sizes were estimated to be 543 Mb and 315 Mb respectively, and a high level of heterozygosity was . O'Brien EA, Zhang Y, Yang L, Wang E, Marie V, Lang BF, Burger G: GOBASEa database of organelle and bacterial genome information. 2006 Jan 24;7:36. doi: 10.1186/1471-2105-7-36. 2007, 21 (1): 44-52. Abstract. doi: 10.1093/nar/gkl780. In IMGD, 132 completely or nearly-completely sequenced mitochondrial genomes and 113,985 mitochondrial gene sequences from 25,747 species were archived. BP developed the interface for Phyloviewer, JP integrated SAP to IMGD and DH conducted mitochondrial genome alignments. Natl Acad. Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PD: DNA barcodes distinguish species of tropical Lepidoptera.
MitoFish: Mitochondrial Genome Database of Fish Epub 2022 Jan 12. 2002, 22 (1): 101-110. Mol Phylogenet Evol. Disclaimer.
The mitochondrial genome: structure, transcription, translation and Sci. 2007, 16 (9): 1957-1968. The bar graph displays the distribution of SNPs in 13 PCGs of three insect species: BO, Bactrocera oleae; DS, Drosophila simulans; RF, Reticulitermes flavipes. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. Damgaard J, Klass KD, Picker MD, Buder G: Phylogeny of the Heelwalkers (Insecta: Mantophasmatodea) based on mtDNA sequences, with evidence for additional taxa in South Africa. The Phyloviewer (http://www.phyloviewer.org/) provides four phylogenetic analysis programs (ClustalW, DNAPARS/PROTPARS, DNAML/PROML, and PHYML [2931]) via a common interface to support phylogenetic studies based on the mitochondrial gene/genome sequences archived in IMGD. Natl Acad. The mtDB provides a unique resource to both medical and human population genetic researchers. Article 2007, 44 (3): 1306-1319. Conversely, reads genuinely arising from the mtDNA genome can be mis-aligned to the NUMTs in the reference genome. The Insect Mitochondrial Genome Database (IMGD) is a new integrated platform that archives the mitochondrial genome sequences from 25,747 hexapod species, including 112 completely sequenced and 20 nearly completed genomes and 113,985 partially sequenced mitochondrial genomes. The middleware platform manages not only BLAST, tRNAScan-SE, and mFold but also six phylogenetic tools managed by Phyloviewer (http://www.phyloviewer.org/).
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