The Experts below are selected from a list of 82188 Experts worldwide ranked by ideXlab platform
Chris Upton - One of the best experts on this subject based on the ideXlab platform.
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Genome annotation transfer utility gatu rapid annotation of viral Genomes using a closely related Reference Genome
BMC Genomics, 2006Co-Authors: Vasily Tcherepanov, Angelika Ehlers, Chris UptonAbstract:Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral Genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics – Canada http://www.virology.ca , we found that researchers were unnecessarily spending time annotating viral Genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU), to transfer annotations from a previously annotated Reference Genome to a new target Genome, thereby greatly reducing this laborious task. GATU transfers annotations from a Reference Genome to a closely related target Genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the Reference Genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated Genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences. GATU greatly simplifies the initial stages of Genome annotation by using a closely related Genome as a Reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring Reference Genome annotations to the target Genome. The program is freely available under the General Public License and can be accessed along with documentation and tutorial from http://www.virology.ca/gatu .
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Genome annotation transfer utility gatu rapid annotation of viral Genomes using a closely related Reference Genome
BMC Genomics, 2006Co-Authors: Vasily Tcherepanov, Angelika Ehlers, Chris UptonAbstract:Background Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral Genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics – Canada http://www.virology.ca, we found that researchers were unnecessarily spending time annotating viral Genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU), to transfer annotations from a previously annotated Reference Genome to a new target Genome, thereby greatly reducing this laborious task.
Scott R Hawley - One of the best experts on this subject based on the ideXlab platform.
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rapid low cost assembly of the drosophila melanogaster Reference Genome using low coverage long read sequencing
G3: Genes Genomes Genetics, 2018Co-Authors: Edwin A Solares, Mahul Chakraborty, Danny E Miller, Shannon Kalsow, Kate Hall, Anoja Perera, J J Emerson, Scott R HawleyAbstract:Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, high-throughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster Reference Genome has revealed that short read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While Genomes assembled using high-coverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited widespread adoption of such sequencing approaches. Here we resequenced the Reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo Genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly with completeness and contiguity comparable to the D. melanogaster Reference assembly. Comparison of our assembly to the Reference assembly of ISO1 uncovered a number of structural variants (SVs), including novel LTR transposable element insertions and duplications affecting genes with developmental, behavioral, and metabolic functions. Collectively, these SVs provide a snapshot of the dynamics of Genome evolution. Furthermore, our assembly and comparison to the D. melanogaster Reference Genome demonstrates that high-quality de novo assembly of Reference Genomes and comprehensive variant discovery using such assemblies are now possible by a single lab for under $1,000 (USD).
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rapid low cost assembly of the drosophila melanogaster Reference Genome using low coverage long read sequencing
bioRxiv, 2018Co-Authors: Edwin A Solares, Mahul Chakraborty, Danny E Miller, Shannon Kalsow, Kate Hall, Anoja Perera, J J Emerson, Scott R HawleyAbstract:Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, high-throughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster Reference Genome has revealed that short-read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While Genomes assembled using high-coverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited the widespread adoption of such sequencing approaches. Here we resequence the Reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hours. Using only reads longer than 1 kb, or 30x coverage, we de novo assemble a highly contiguous Genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly with completeness and contiguity comparable to the D. melanogaster Reference assembly. Surprisingly, comparison of our assembly to the Reference assembly of ISO1 uncovered a number of structural variants, including novel LTR transposable element insertions and duplications affecting genes with developmental, behavioral, and metabolic functions. Collectively, these structural variants provide a rare snapshot of the dynamics of metazoan Genome evolution. Furthermore, our assembly and comparison to the D. melanogaster Reference Genome demonstrates that Reference-quality de novo assembly of metazoan Genomes and comprehensive variant discovery using such assemblies are now possible for under $1,000 USD.
Vasily Tcherepanov - One of the best experts on this subject based on the ideXlab platform.
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Genome annotation transfer utility gatu rapid annotation of viral Genomes using a closely related Reference Genome
BMC Genomics, 2006Co-Authors: Vasily Tcherepanov, Angelika Ehlers, Chris UptonAbstract:Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral Genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics – Canada http://www.virology.ca , we found that researchers were unnecessarily spending time annotating viral Genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU), to transfer annotations from a previously annotated Reference Genome to a new target Genome, thereby greatly reducing this laborious task. GATU transfers annotations from a Reference Genome to a closely related target Genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the Reference Genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated Genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences. GATU greatly simplifies the initial stages of Genome annotation by using a closely related Genome as a Reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring Reference Genome annotations to the target Genome. The program is freely available under the General Public License and can be accessed along with documentation and tutorial from http://www.virology.ca/gatu .
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Genome annotation transfer utility gatu rapid annotation of viral Genomes using a closely related Reference Genome
BMC Genomics, 2006Co-Authors: Vasily Tcherepanov, Angelika Ehlers, Chris UptonAbstract:Background Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral Genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics – Canada http://www.virology.ca, we found that researchers were unnecessarily spending time annotating viral Genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU), to transfer annotations from a previously annotated Reference Genome to a new target Genome, thereby greatly reducing this laborious task.
Yun Sung Cho - One of the best experts on this subject based on the ideXlab platform.
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an ethnically relevant consensus korean Reference Genome is a step towards personal Reference Genomes
Nature Communications, 2016Co-Authors: Yun Sung Cho, Hwajung Kim, Hakmin Kim, Sungwoong Jho, Jehoon Jun, Yongjoo Lee, Kyun Shik Chae, Chang Geun KimAbstract:Human Genomes are routinely compared against a universal Reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal Reference. Here we report a hybrid assembly of a Korean Reference Genome (KOREF) for constructing personal and ethnic References by combining sequencing and mapping methods. We also build its consensus variome Reference, providing information on millions of variants from 40 additional ethnically homogeneous Genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus Reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population Genome projects, the leveraging of ethnicity-specific Genome assemblies as well as the human Reference Genome will accelerate mapping all human Genome diversity. The utility of a universal Reference sequence for human Genome comparisons is dependent on the ethnic origins of the individuals being sequenced. Here the authors report a Korean Reference Genome and consensus variome, and show that an ethnically-relevant Reference can improve variant detection.
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ethnically relevant consensus korean Reference Genome towards personal Reference Genomes
bioRxiv, 2016Co-Authors: Yun Sung Cho, Hwajung Kim, Sungwoong Jho, Jehoon Jun, Yongjoo Lee, Kyun Shik Chae, Chang Geun Kim, Sangsoo Kim, Anders Eriksson, Jeremy S EdwardsAbstract:Human Genomes are routinely compared against a universal Reference. However, this strategy could miss population-specific or personal genomic variations, which may be detected more efficiently using an ethnically-relevant and/or a personal Reference. Here we report a hybrid assembly of Korean Reference (KOREF) as a pilot case for constructing personal and ethnic References by combining sequencing and mapping methods. KOREF is also the first consensus variome Reference, providing information on millions of variants from additional ethnically homogeneous personal Genomes. We found that this ethnically-relevant consensus Reference was beneficial for efficiently detecting variants. Systematic comparison of KOREF with previously established human assemblies showed the importance of assembly quality, suggesting the necessity of using new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population Genome projects, the leveraging of ethnicity-specific Genome assemblies as well as the human Reference Genome will accelerate mapping all human Genome diversity.
Angelika Ehlers - One of the best experts on this subject based on the ideXlab platform.
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Genome annotation transfer utility gatu rapid annotation of viral Genomes using a closely related Reference Genome
BMC Genomics, 2006Co-Authors: Vasily Tcherepanov, Angelika Ehlers, Chris UptonAbstract:Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral Genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics – Canada http://www.virology.ca , we found that researchers were unnecessarily spending time annotating viral Genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU), to transfer annotations from a previously annotated Reference Genome to a new target Genome, thereby greatly reducing this laborious task. GATU transfers annotations from a Reference Genome to a closely related target Genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the Reference Genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated Genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences. GATU greatly simplifies the initial stages of Genome annotation by using a closely related Genome as a Reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring Reference Genome annotations to the target Genome. The program is freely available under the General Public License and can be accessed along with documentation and tutorial from http://www.virology.ca/gatu .
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Genome annotation transfer utility gatu rapid annotation of viral Genomes using a closely related Reference Genome
BMC Genomics, 2006Co-Authors: Vasily Tcherepanov, Angelika Ehlers, Chris UptonAbstract:Background Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral Genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics – Canada http://www.virology.ca, we found that researchers were unnecessarily spending time annotating viral Genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU), to transfer annotations from a previously annotated Reference Genome to a new target Genome, thereby greatly reducing this laborious task.
