Analysis of Drosophila Species Genome Size and Satellite DNA
... Accepted for publication June 20, 2007 ABSTRACT The size of eukaryotic genomes can vary by several orders of magnitude, yet genome size does not correlate with the number of genes nor with the size or complexity of the organism. Although ‘‘whole’’-genome sequences, such as those now available for 12 ...
... Accepted for publication June 20, 2007 ABSTRACT The size of eukaryotic genomes can vary by several orders of magnitude, yet genome size does not correlate with the number of genes nor with the size or complexity of the organism. Although ‘‘whole’’-genome sequences, such as those now available for 12 ...
Reconciling the many faces of lateral gene transfer
... as horizontally acquired because related fim genes are found at multiple locations in many enteric bacterial genomes. In addition to gene organization, other biological information can be used to interpret patterns of gene transfer events. For example, whereas only half of the genes in a six-gene cl ...
... as horizontally acquired because related fim genes are found at multiple locations in many enteric bacterial genomes. In addition to gene organization, other biological information can be used to interpret patterns of gene transfer events. For example, whereas only half of the genes in a six-gene cl ...
Consistent Errors in First Strand cDNA Due to Random Hexamer
... mispriming induced mismatches, however, their origin is not described. For example, empirically derived filtering parameters for putative somatic mutations used in Varscan 2 exclude the first ten bases of reads [15], and 5’ trimming has been applied to Illumina RNA-seq reads showing an increased N50 ...
... mispriming induced mismatches, however, their origin is not described. For example, empirically derived filtering parameters for putative somatic mutations used in Varscan 2 exclude the first ten bases of reads [15], and 5’ trimming has been applied to Illumina RNA-seq reads showing an increased N50 ...
Identifying key developments, issues and
... are intended to facilitate researchers to precisely alter genes or genomes in many species. Genome editing has been said to be revolutionising biology. 2 If these techniques continue to show success, it will be possible to alter or replace virtually any component of any genome; from a single base pa ...
... are intended to facilitate researchers to precisely alter genes or genomes in many species. Genome editing has been said to be revolutionising biology. 2 If these techniques continue to show success, it will be possible to alter or replace virtually any component of any genome; from a single base pa ...
PDF file
... • Samples genotyped using Axiom 132 K SNP array • QC filtering of SNPs and individuals (Mendel error, MAF, etc.) 111 K SNPs retained 29 sires, 61 dams, 534 offspring ...
... • Samples genotyped using Axiom 132 K SNP array • QC filtering of SNPs and individuals (Mendel error, MAF, etc.) 111 K SNPs retained 29 sires, 61 dams, 534 offspring ...
PDF
... recently launched interlaboratory project that aims to sequence over the next 5 years the genomes of 5,000 insects and related arthropod species important for agriculture, medicine and biotechnology [37] should be highly useful for such genomic screens. On the other hand, transposase-mediated remobi ...
... recently launched interlaboratory project that aims to sequence over the next 5 years the genomes of 5,000 insects and related arthropod species important for agriculture, medicine and biotechnology [37] should be highly useful for such genomic screens. On the other hand, transposase-mediated remobi ...
A systematic genome-wide analysis of zebrafish protein
... changes detectable during the first 5 dpf in live embryos. Subtle phenotypes that require further intervention, such as immunohistochemistry, are not currently assayed. Finally, the teleost-specific genome duplication might cause paralogue redundancy. While this is possible there are few examples of ...
... changes detectable during the first 5 dpf in live embryos. Subtle phenotypes that require further intervention, such as immunohistochemistry, are not currently assayed. Finally, the teleost-specific genome duplication might cause paralogue redundancy. While this is possible there are few examples of ...
Retrovirus Integration Database (RID): a public database for
... using NCBI genome. This local gene annotation database is derived from NCBI genomes (http://www.ncbi. nlm.nih.gov/genome/). If an integration site is not in a gene, then the nearest genes in both directions were mapped and stored in RID. All gene annotations were based on human genome build GRCH37/h ...
... using NCBI genome. This local gene annotation database is derived from NCBI genomes (http://www.ncbi. nlm.nih.gov/genome/). If an integration site is not in a gene, then the nearest genes in both directions were mapped and stored in RID. All gene annotations were based on human genome build GRCH37/h ...
Influence of the environment and probes on rapid DNA sequencing
... by sampling the current with the driving field off. The distributions of these currents, with this particular pore geometry, for all four bases are shown in the top section of Figure 3, assuming each current is measured instantaneously.∗∗ We can see that these distributions are unique, but overlappi ...
... by sampling the current with the driving field off. The distributions of these currents, with this particular pore geometry, for all four bases are shown in the top section of Figure 3, assuming each current is measured instantaneously.∗∗ We can see that these distributions are unique, but overlappi ...
docx
... for an interrogating base position includes five probes: one probe to hybridise to the WT, three probes to detect three possible single base-pair mutations, and one probe to detect single deletion. There are at least 24 probe sets for each nucleotide position, including both sense and anti-sense pro ...
... for an interrogating base position includes five probes: one probe to hybridise to the WT, three probes to detect three possible single base-pair mutations, and one probe to detect single deletion. There are at least 24 probe sets for each nucleotide position, including both sense and anti-sense pro ...
Advancing Science with DNA Sequence Finding the genes in
... Advancing Science with DNA Sequence ...
... Advancing Science with DNA Sequence ...
genetic testing - NYU School of Medicine
... commonly used genetic tests only provide information about those genes or chromosomes that doctors know are associated with disease. Whole Genome Sequencing The genome is the entire set of genetic instructions found in a cell. In humans, the genome consists of 23 pairs of chromosomes, found in the n ...
... commonly used genetic tests only provide information about those genes or chromosomes that doctors know are associated with disease. Whole Genome Sequencing The genome is the entire set of genetic instructions found in a cell. In humans, the genome consists of 23 pairs of chromosomes, found in the n ...
Comparison of genes among cereals
... genomes, rice (430 Mb), sorghum (770 Mb), maize (2700 Mb), and wheat (16 000 Mb) [19] and the evolutionary divergence time of 60 million years for these species [17,20]. The initial work on the colinearity of genetic markers was reinforced when it was discovered that quantitative loci for agronomic ...
... genomes, rice (430 Mb), sorghum (770 Mb), maize (2700 Mb), and wheat (16 000 Mb) [19] and the evolutionary divergence time of 60 million years for these species [17,20]. The initial work on the colinearity of genetic markers was reinforced when it was discovered that quantitative loci for agronomic ...
Taq polymerase errors in PCR: Frequency and management
... • Well studied by Chen and colleagues (1991, Mutation Research) • Topic: mutations in the human adenine phosphoribosyltransferase genes = HPTR deficiency that cause a kidney disease 1. Cloning and sequencing of HPRT gene from human DNA library (reference sequence) 2. Cloning of HPRT PCR products and ...
... • Well studied by Chen and colleagues (1991, Mutation Research) • Topic: mutations in the human adenine phosphoribosyltransferase genes = HPTR deficiency that cause a kidney disease 1. Cloning and sequencing of HPRT gene from human DNA library (reference sequence) 2. Cloning of HPRT PCR products and ...
CURRICULUM VITAE - Oxford University Statistics
... recombination occurs very unevenly across the genome, that most recombination occurs in narrow hotspots, and that recombination rates vary rapidly over evolutionary time. I have developed methods to detect such hotspots from sequence data, based on using the coalescent with recombination as a model ...
... recombination occurs very unevenly across the genome, that most recombination occurs in narrow hotspots, and that recombination rates vary rapidly over evolutionary time. I have developed methods to detect such hotspots from sequence data, based on using the coalescent with recombination as a model ...
MS Word - VCU Secrets of the Sequence
... Although other videos in this Secrets of the Sequence series present information obtained from the mapping of the human genome, this video explains what “mapping the genome” means. It answers the question, “Why do we map a species and what information do we get from this map?” The map tells us which ...
... Although other videos in this Secrets of the Sequence series present information obtained from the mapping of the human genome, this video explains what “mapping the genome” means. It answers the question, “Why do we map a species and what information do we get from this map?” The map tells us which ...
Reference genome sequence of the model plant Setaria
... population through eight generations of single-seed descent. This population was mapped with 992 single-nucleotide polymorphism (SNP) markers (Supplementary Note 1) distributed at ~400-kb intervals across the version 1.0 assembly. The 992 mapped SNPs were distributed over 73 scaffolds, leaving 6.7 M ...
... population through eight generations of single-seed descent. This population was mapped with 992 single-nucleotide polymorphism (SNP) markers (Supplementary Note 1) distributed at ~400-kb intervals across the version 1.0 assembly. The 992 mapped SNPs were distributed over 73 scaffolds, leaving 6.7 M ...
Gene Regulation
... A set of 481 vertebrate PWMs frm Transfac 7.2 was used for the analysis. PWMs were grouped into 229 families. The genome-wide multiple alignment was done for the human, mouse and rat genomes by the MULTIZ program. Only the regions within MULTIZ alignment were considered in the later part of the stud ...
... A set of 481 vertebrate PWMs frm Transfac 7.2 was used for the analysis. PWMs were grouped into 229 families. The genome-wide multiple alignment was done for the human, mouse and rat genomes by the MULTIZ program. Only the regions within MULTIZ alignment were considered in the later part of the stud ...
DNA SEQUENCING (using a Li
... methods, and their derivations. Both methods were first described in 1977. The first method (Maxam and Gilbert 1977) is based on specific chemical degradation of the DNA. The DNA is first end-labeled using 35s or 33P, followed by separation of the two strands on a gel. Four aliquots of the desired s ...
... methods, and their derivations. Both methods were first described in 1977. The first method (Maxam and Gilbert 1977) is based on specific chemical degradation of the DNA. The DNA is first end-labeled using 35s or 33P, followed by separation of the two strands on a gel. Four aliquots of the desired s ...
S1 Text.
... in the 500 bp range, about 10 times stronger and with a tighter length distribution than the template library. The amplified library was then purified with AMPure XP beads with a final elution in 30 µL elution buffer. The DNA concentration of the purified library was measured with a Qubit fluoromete ...
... in the 500 bp range, about 10 times stronger and with a tighter length distribution than the template library. The amplified library was then purified with AMPure XP beads with a final elution in 30 µL elution buffer. The DNA concentration of the purified library was measured with a Qubit fluoromete ...
Case Study: Visualization of annotated DNA sequences
... semantic zooming and annotation comparison, but zooming and panning is not real-time (VIII) and the browser does not support DNA sequence comparisons (X). Therefore, we have developed a DNA visualization tool that fulfills all defined requirements. DNAVis is written in C++ and runs on both Windows a ...
... semantic zooming and annotation comparison, but zooming and panning is not real-time (VIII) and the browser does not support DNA sequence comparisons (X). Therefore, we have developed a DNA visualization tool that fulfills all defined requirements. DNAVis is written in C++ and runs on both Windows a ...
Large-scale association studies
... – most people us 2.5 million HapMap Phase II SNPs – starting to use 38 million 1000 Genomes SNPs – for additive genetic model, doesn’t matter whether SNPs are measured or imputed. – slightly more work needed for non-additive genetic models or SNP:SNP interaction models ...
... – most people us 2.5 million HapMap Phase II SNPs – starting to use 38 million 1000 Genomes SNPs – for additive genetic model, doesn’t matter whether SNPs are measured or imputed. – slightly more work needed for non-additive genetic models or SNP:SNP interaction models ...
Part 2 - Laboratory of Aquaculture & Artemia Reference Center
... system for its survival even under extreme conditions. Artemia seems to be a promising system for stress response studies as observed in our laboratory since it shows a swift adaptation to harsh environments. A variety of Heat shock proteins (HSPs) were expressed which when characterized will give a ...
... system for its survival even under extreme conditions. Artemia seems to be a promising system for stress response studies as observed in our laboratory since it shows a swift adaptation to harsh environments. A variety of Heat shock proteins (HSPs) were expressed which when characterized will give a ...
Whole genome sequencing
Whole genome sequencing (also known as full genome sequencing, complete genome sequencing, or entire genome sequencing) is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.Whole genome sequencing should not be confused with DNA profiling, which only determines the likelihood that genetic material came from a particular individual or group, and does not contain additional information on genetic relationships, origin or susceptibility to specific diseases. Also unlike full genome sequencing, SNP genotyping covers less than 0.1% of the genome. Almost all truly complete genomes are of microbes; the term ""full genome"" is thus sometimes used loosely to mean ""greater than 95%"". The remainder of this article focuses on nearly complete human genomes.High-throughput genome sequencing technologies have largely been used as a research tool and are currently being introduced in the clinics. In the future of personalized medicine, whole genome sequence data will be an important tool to guide therapeutic intervention. The tool of gene sequencing at SNP level is also used to pinpoint functional variants from association studies and improve the knowledge available to researchers interested in evolutionary biology, and hence may lay the foundation for predicting disease susceptibility and drug response.