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functionless dna - Semantic Scholar
... functional. From an evolutionary viewpoint, a function can be assigned to a DNA sequence if and only if it is possible to destroy it (Graur et al. 2013). All functional entities in the universe can be rendered nonfunctional by the ravages of time, entropy, mutation, and what have you. Unless a genom ...
... functional. From an evolutionary viewpoint, a function can be assigned to a DNA sequence if and only if it is possible to destroy it (Graur et al. 2013). All functional entities in the universe can be rendered nonfunctional by the ravages of time, entropy, mutation, and what have you. Unless a genom ...
UV-Targeted Dinucleotides Are Not Depleted in Light
... pyrimidine dinucleotide content. Pyrimidine dinucleotides are the direct targets of UVb wavelengths, and if UV light has a major impact on genomes, we can expect highly exposed microorganisms to display significant depletion of all 4 pyrimidine dinucleotides (CpC, CpT, TpC, and TpT). Last but not le ...
... pyrimidine dinucleotide content. Pyrimidine dinucleotides are the direct targets of UVb wavelengths, and if UV light has a major impact on genomes, we can expect highly exposed microorganisms to display significant depletion of all 4 pyrimidine dinucleotides (CpC, CpT, TpC, and TpT). Last but not le ...
Evolutionary Genomics of Fast Evolving Tunicates
... Key words: positive selection, genome plasticity, Oikopleura dioica, Ciona. ...
... Key words: positive selection, genome plasticity, Oikopleura dioica, Ciona. ...
Application Note: Targeted sequencing and chromosomal haplotype
... with ~4 segments per read. The schematic in Figure 3 illustrates the general structure of the reads and how they mapped to the reference. Mapped reads generated with the Targeted TLA to BRCA1 fully cover the BRCA1 region (Figure 4), with heterozygous SNPs clearly visible from the TLA data (Figure 5) ...
... with ~4 segments per read. The schematic in Figure 3 illustrates the general structure of the reads and how they mapped to the reference. Mapped reads generated with the Targeted TLA to BRCA1 fully cover the BRCA1 region (Figure 4), with heterozygous SNPs clearly visible from the TLA data (Figure 5) ...
Touring Ensembl: A practical guide to genome browsing Open Access
... browsers provide an aid to the researcher by importing biological data from various sources and presenting these data in an integrated way. Three multi-species genome browsers are widely used by the scientific community: the UCSC genome browser, NCBI Map Viewer, and Ensembl (Table 1). Others include ...
... browsers provide an aid to the researcher by importing biological data from various sources and presenting these data in an integrated way. Three multi-species genome browsers are widely used by the scientific community: the UCSC genome browser, NCBI Map Viewer, and Ensembl (Table 1). Others include ...
Lesson Overview
... an individual may be born with three copies of that chromosome. This condition is known as a trisomy, meaning “three bodies.” The most common form of trisomy, involving three copies of chromosome 21, is Down syndrome, which is often characterized by mild to severe mental retardation and a high frequ ...
... an individual may be born with three copies of that chromosome. This condition is known as a trisomy, meaning “three bodies.” The most common form of trisomy, involving three copies of chromosome 21, is Down syndrome, which is often characterized by mild to severe mental retardation and a high frequ ...
Testing enhancers predicted by high constraint
... Identifying the sequences that direct the spatial and temporal expression of genes and defining their function in vivo remains a significant challenge in the annotation of vertebrate genomes. One major obstacle is the lack of experimentally validated training sets. In this study, we made use of extr ...
... Identifying the sequences that direct the spatial and temporal expression of genes and defining their function in vivo remains a significant challenge in the annotation of vertebrate genomes. One major obstacle is the lack of experimentally validated training sets. In this study, we made use of extr ...
S1 Appendix.
... often annotation-specific, and should be optimized if custom annotation files are used. The current script can be used to extract information about genes (whole transcripts), coding sequences, ncRNAs, 3’ untranslated regions (UTRs), 5’ UTRs and tRNAs. In cerevisiae genome files, in addition to codin ...
... often annotation-specific, and should be optimized if custom annotation files are used. The current script can be used to extract information about genes (whole transcripts), coding sequences, ncRNAs, 3’ untranslated regions (UTRs), 5’ UTRs and tRNAs. In cerevisiae genome files, in addition to codin ...
TregouetD_EGEE3-presentation
... Estimate the SNP allele frequencies in cases and controls and calculate the corresponding statistical test yielding a pvalue • SNP definition Genetic variation in a DNA sequence that occurs when a single nucleotide (~ base: A,C,G,T ) in a genome is altered. Often considered as a binary 0/1 variable ...
... Estimate the SNP allele frequencies in cases and controls and calculate the corresponding statistical test yielding a pvalue • SNP definition Genetic variation in a DNA sequence that occurs when a single nucleotide (~ base: A,C,G,T ) in a genome is altered. Often considered as a binary 0/1 variable ...
Analyzing Genomic Mappings with the GOLAM Framework
... processing cost to each OLAP query. So, the approach we are currently pursuing in GOLAM is to materialize the full genome space when the Map operation is executed, and then extract the GTF files that cover all the missing data needed to answer each OLAP query. In this scenario, the finest granularit ...
... processing cost to each OLAP query. So, the approach we are currently pursuing in GOLAM is to materialize the full genome space when the Map operation is executed, and then extract the GTF files that cover all the missing data needed to answer each OLAP query. In this scenario, the finest granularit ...
Introduction to RNA sequencing
... Why sequence RNA (versus DNA)? • Interpreting mutations that do not have an obvious effect on protein sequence – ‘Regulatory’ mutations that affect what mRNA isoform is expressed and how much • e.g. splice sites, promoters, exonic/intronic splicing motifs, etc. ...
... Why sequence RNA (versus DNA)? • Interpreting mutations that do not have an obvious effect on protein sequence – ‘Regulatory’ mutations that affect what mRNA isoform is expressed and how much • e.g. splice sites, promoters, exonic/intronic splicing motifs, etc. ...
Analysis of mRNA - quantitation (contd)
... 1. (8 points) The coffee berry borer (Hypothenemus hampei) is a plague that affects coffee crops. H. hampei is an exceptional organism, because it consumes so much caffeine that it would kill any other insect - it is exposed to the equivalent of 500 espressos per day. The closely related species, H ...
... 1. (8 points) The coffee berry borer (Hypothenemus hampei) is a plague that affects coffee crops. H. hampei is an exceptional organism, because it consumes so much caffeine that it would kill any other insect - it is exposed to the equivalent of 500 espressos per day. The closely related species, H ...
Precise insertion and guided editing of higher plant
... off target sites within the rice genome, both of which contained a 4 bp mismatch. Both genomic regions were amplified via PCR from multiple GE0001 events as well as from wild type rice. These fragments were subcloned, sequenced via Sanger sequencing and compared to the wild type sequences. No off-ta ...
... off target sites within the rice genome, both of which contained a 4 bp mismatch. Both genomic regions were amplified via PCR from multiple GE0001 events as well as from wild type rice. These fragments were subcloned, sequenced via Sanger sequencing and compared to the wild type sequences. No off-ta ...
Shastry, B.S. 2002. SNP alleles in human disease and evolution
... SNPs in gene discovery Once the map of these SNPs is confirmed, they can be used for evolutionary biology studies, gene discovery and mapping, prediction of drug and environmental response, diagnostic tests, heterogeneity testing, and association studies (Gray et al. 2000; Schork et al. 2000). For t ...
... SNPs in gene discovery Once the map of these SNPs is confirmed, they can be used for evolutionary biology studies, gene discovery and mapping, prediction of drug and environmental response, diagnostic tests, heterogeneity testing, and association studies (Gray et al. 2000; Schork et al. 2000). For t ...
Physical Mapping of Important Trait Loci in the Pig
... the genetic background of inherited diseases. An important goal is also to develop new and more specific pharmaceuticals with less side effects. The drug industry can utilize the genome information in order to find candidate drug targets. It will also be possible to create individual treatments, sin ...
... the genetic background of inherited diseases. An important goal is also to develop new and more specific pharmaceuticals with less side effects. The drug industry can utilize the genome information in order to find candidate drug targets. It will also be possible to create individual treatments, sin ...
All Alus are approximately 300 bp in length and derive
... hundreds of thousands of Alu copies have accumulated in primates since their separation from other vertebrate groups about 65 million years ago. • Once an Alu inserts at a chromosome locus, it can copy itself for transposition, but there is no evidence that it is ever excised or lost from a chromoso ...
... hundreds of thousands of Alu copies have accumulated in primates since their separation from other vertebrate groups about 65 million years ago. • Once an Alu inserts at a chromosome locus, it can copy itself for transposition, but there is no evidence that it is ever excised or lost from a chromoso ...
Gene Loss and Evolutionary Rates Following Whole
... Out of 2,371 human genes with a clear orthology relation to mapped Tetraodon genes, 364 have a phylogenetic profile typical of the WGD in Tetraodon (see Materials and Methods). This gives an estimate of 15% of gene pairs retained after the WGD, that is, loss of one of the paralogs in 85% of pairs. T ...
... Out of 2,371 human genes with a clear orthology relation to mapped Tetraodon genes, 364 have a phylogenetic profile typical of the WGD in Tetraodon (see Materials and Methods). This gives an estimate of 15% of gene pairs retained after the WGD, that is, loss of one of the paralogs in 85% of pairs. T ...
Here - Personal Genome Project Study Guide
... caused by mutations in the DMD gene. The DMD gene codes for a protein called dystrophin that is necessary for muscle cells to maintain their shape. When this protein is missing, muscle cells literally burst as material from outside the cell membrane leaks in, raising cell pressure. Mutations in the ...
... caused by mutations in the DMD gene. The DMD gene codes for a protein called dystrophin that is necessary for muscle cells to maintain their shape. When this protein is missing, muscle cells literally burst as material from outside the cell membrane leaks in, raising cell pressure. Mutations in the ...
Table S1.
... Table S1 – Overview of prediction attributes 0. General remarks In order to make the attributes comparable between multiple CpG islands and windows of different sizes, most attributes are averages (or standard deviations, etc.) over the window of interest, standardized to a 1kb window. Variance stab ...
... Table S1 – Overview of prediction attributes 0. General remarks In order to make the attributes comparable between multiple CpG islands and windows of different sizes, most attributes are averages (or standard deviations, etc.) over the window of interest, standardized to a 1kb window. Variance stab ...
"What is a gene, in the post-ENCODE era?"
... The classical view of a gene as a discrete element in the genome has been shaken by ENCODE The ENCODE consortium recently completed its characterization of 1% of the human genome by various high-throughput experimental and computational techniques designed to characterize functional elements (The EN ...
... The classical view of a gene as a discrete element in the genome has been shaken by ENCODE The ENCODE consortium recently completed its characterization of 1% of the human genome by various high-throughput experimental and computational techniques designed to characterize functional elements (The EN ...
What is a gene, post-ENCODE? History and updated
... The classical view of a gene as a discrete element in the genome has been shaken by ENCODE The ENCODE consortium recently completed its characterization of 1% of the human genome by various high-throughput experimental and computational techniques designed to characterize functional elements (The EN ...
... The classical view of a gene as a discrete element in the genome has been shaken by ENCODE The ENCODE consortium recently completed its characterization of 1% of the human genome by various high-throughput experimental and computational techniques designed to characterize functional elements (The EN ...
What is a gene, post-ENCODE? History and updated definition
... It was the solution of the three-dimensional structure of DNA by Watson and Crick in 1953 (Watson and Crick 1953) that explained how DNA could function as the molecule of heredity. Base pairing explained how genetic information could be copied, and the existence of two strands explained how occasion ...
... It was the solution of the three-dimensional structure of DNA by Watson and Crick in 1953 (Watson and Crick 1953) that explained how DNA could function as the molecule of heredity. Base pairing explained how genetic information could be copied, and the existence of two strands explained how occasion ...
towards synthetic plant genomes, transcriptomes and epigenomes
... It is possible to target individual sequence motives within genomes by using synthetic DNA-binding domains. This one-dimensional approach has been used successfully in plants to induce mutations or for the transcriptional regulation of single genes. When the CRISPR (clustered regularly interspaced s ...
... It is possible to target individual sequence motives within genomes by using synthetic DNA-binding domains. This one-dimensional approach has been used successfully in plants to induce mutations or for the transcriptional regulation of single genes. When the CRISPR (clustered regularly interspaced s ...
Human Genome Project
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The Human Genome Project (HGP) is an international scientific research project with the goal of determining the sequence of chemical base pairs which make up human DNA, and of identifying and mapping all of the genes of the human genome from both a physical and functional standpoint. It remains the world's largest collaborative biological project. The project was proposed and funded by the US government; planning started in 1984, got underway in 1990, and was declared complete in 2003. A parallel project was conducted outside of government by the Celera Corporation, or Celera Genomics, which was formally launched in 1998. Most of the government-sponsored sequencing was performed in twenty universities and research centers in the United States, the United Kingdom, Japan, France, Germany, and China.The Human Genome Project originally aimed to map the nucleotides contained in a human haploid reference genome (more than three billion). The ""genome"" of any given individual is unique; mapping ""the human genome"" involves sequencing multiple variations of each gene.