a role for mitochondrial enzymes in inherited neoplasia and beyond
... have lost the remaining wild-type allele 8,15,21–23. Further research is required to determine how loss of the wild-type allele occurs. The observation that germline mutations in genes that encode mitochondrial enzymes are associated with inherited cancer syndromes is relatively recent. In addition, ...
... have lost the remaining wild-type allele 8,15,21–23. Further research is required to determine how loss of the wild-type allele occurs. The observation that germline mutations in genes that encode mitochondrial enzymes are associated with inherited cancer syndromes is relatively recent. In addition, ...
Horizontal transfer of non-LTR retrotransposons: artifact or rare event
... for HT detection. Multiple TEs lineages can be present within genomes. Moreover, TEs are multicopy components of genomes. Comparisons of paralogous TE copies instead of orthologs along with varying rates of their sequence evolution are the main sources for incongruence in phylogenetic analysis, whic ...
... for HT detection. Multiple TEs lineages can be present within genomes. Moreover, TEs are multicopy components of genomes. Comparisons of paralogous TE copies instead of orthologs along with varying rates of their sequence evolution are the main sources for incongruence in phylogenetic analysis, whic ...
A physical map of the genome of Hmmophilus
... (GCC’GGC) gave reproducible results, each generating 15-23 large fragments. ApaI (GGGCC’C) gave inconsistent results and was not used. Two other enzymes with recognition sequences comprising only G-C base pairs are SacII (CCGC’GG) and NarI (GG’CGCC); these were not useful for our mapping project. Sa ...
... (GCC’GGC) gave reproducible results, each generating 15-23 large fragments. ApaI (GGGCC’C) gave inconsistent results and was not used. Two other enzymes with recognition sequences comprising only G-C base pairs are SacII (CCGC’GG) and NarI (GG’CGCC); these were not useful for our mapping project. Sa ...
Detection of Mosaicism by Augmented Exome
... strategies. However, routine detection of mosaicism in conventional genome and exome sequencing is hampered by multiple factors. Assumptions inherent to genotyping and filtration strategies utilized by both genome and exome analysis often result in the dismissal or outright failure to call variants ...
... strategies. However, routine detection of mosaicism in conventional genome and exome sequencing is hampered by multiple factors. Assumptions inherent to genotyping and filtration strategies utilized by both genome and exome analysis often result in the dismissal or outright failure to call variants ...
Multifractal characterisation of length sequences of coding and
... There has been considerable interest in the 3nding of long-range correlation (LRC) in DNA sequences at this level. Li et al. [2,3] found that the spectral density of a DNA sequence containing mostly introns shows 1=f behaviour, which indicates the presence of LRC. The correlation properties of codi ...
... There has been considerable interest in the 3nding of long-range correlation (LRC) in DNA sequences at this level. Li et al. [2,3] found that the spectral density of a DNA sequence containing mostly introns shows 1=f behaviour, which indicates the presence of LRC. The correlation properties of codi ...
Enhanced Detection of Longer Insertions and Deletions in Clinical
... found in the human genome and substantial amount of research, such as that by the International HapMap Consortium, has been focused on accurately mapping and identifying SNVs for human genetic variation studies [8]. However, in spite of being the second most common type of genomic alterations [9], i ...
... found in the human genome and substantial amount of research, such as that by the International HapMap Consortium, has been focused on accurately mapping and identifying SNVs for human genetic variation studies [8]. However, in spite of being the second most common type of genomic alterations [9], i ...
Bioinformatics Dr. Víctor Treviño Pabellón Tec
... a tree is referred to as the tree length. The tree is also a bifurcating or binary tree, in that only two branches emanate from each node. Trees can have more than one branch emanating from a node if the events separating taxa are so close that they cannot be resolved, or to simplify the tree. The u ...
... a tree is referred to as the tree length. The tree is also a bifurcating or binary tree, in that only two branches emanate from each node. Trees can have more than one branch emanating from a node if the events separating taxa are so close that they cannot be resolved, or to simplify the tree. The u ...
Chapter 12
... Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Recall how a bacterium defends itself when a bacteriophage injects its DNA into a bacterium… The bacterium has enzymes called restriction enzymes that attempt to cut up the bacteriophage DNA befo ...
... Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Recall how a bacterium defends itself when a bacteriophage injects its DNA into a bacterium… The bacterium has enzymes called restriction enzymes that attempt to cut up the bacteriophage DNA befo ...
here - Genomes Unzipped
... identical to those reported by Li et al., though we found a few differences between the sites reported by Li et al. [1] and our analysis. For example, Li et al.[1] report an RDD site at chromosome 4, position 3,9141,595; as far as we can tell, all of the mismatching bases at that site have a low seq ...
... identical to those reported by Li et al., though we found a few differences between the sites reported by Li et al. [1] and our analysis. For example, Li et al.[1] report an RDD site at chromosome 4, position 3,9141,595; as far as we can tell, all of the mismatching bases at that site have a low seq ...
Structural variations in the human genome
... many (many, many) bacteria has been unraveled (38). Still, understanding the human genome remains the ultimate goal. The sequence of the human genome differs tremendously among individuals (2,3). These differences range from single nucleotides to gross alterations. All of these alterations can have ...
... many (many, many) bacteria has been unraveled (38). Still, understanding the human genome remains the ultimate goal. The sequence of the human genome differs tremendously among individuals (2,3). These differences range from single nucleotides to gross alterations. All of these alterations can have ...
Goldmine: Integrating information to place sets of genomic ranges
... compare the context proportions of different subsets. To demonstrate Goldmine on a larger scale, we show how to use the package to annotate the genomic contexts for each factor in the ENCODE ChIP-seq supertrack and compare contexts among all 161 factors. First, we will obtain the ENCODE supertrack c ...
... compare the context proportions of different subsets. To demonstrate Goldmine on a larger scale, we show how to use the package to annotate the genomic contexts for each factor in the ENCODE ChIP-seq supertrack and compare contexts among all 161 factors. First, we will obtain the ENCODE supertrack c ...
Kuijper et al JEB
... males. However, it will typically not achieve fixation, as the fitness cost for females (which transmit the majority of mitochondria) rises markedly with increasing frequency of Cm (dashed line for wm and solid line for wf in Fig. 2b). Consequently, polymorphism is expected to occur in the presence ...
... males. However, it will typically not achieve fixation, as the fitness cost for females (which transmit the majority of mitochondria) rises markedly with increasing frequency of Cm (dashed line for wm and solid line for wf in Fig. 2b). Consequently, polymorphism is expected to occur in the presence ...
#2
... human and chimpanzee, we aligned 14.3 Mb of orthologous noncoding DNA sequences from human, chimpanzee, and baboon (Methods). Subsequently, human chromosomes were split into 1 Mb non-overlapping windows (referred to as loci). We retained 36 loci dispersed over 12 autosomal chromosomes, each of which ...
... human and chimpanzee, we aligned 14.3 Mb of orthologous noncoding DNA sequences from human, chimpanzee, and baboon (Methods). Subsequently, human chromosomes were split into 1 Mb non-overlapping windows (referred to as loci). We retained 36 loci dispersed over 12 autosomal chromosomes, each of which ...
click to - White Rose Research Online
... recent study produced low coverage sequence data for 199 B. rapa and 119 B. oleracea accessions to identify SNPs and trace parallel selection signals in the two subgenomes (Cheng et al. 2016). Regions undergoing positive selection could be identified (25 in B. rapa and 58 in B. oleracea), out of whi ...
... recent study produced low coverage sequence data for 199 B. rapa and 119 B. oleracea accessions to identify SNPs and trace parallel selection signals in the two subgenomes (Cheng et al. 2016). Regions undergoing positive selection could be identified (25 in B. rapa and 58 in B. oleracea), out of whi ...
Table S1.
... Only genes are taken into account that overlap by at least one base pair with window. Attributes are then calculated at exon level for each exon that fulfils the patch overlap definition (overlap >25% of exon length or >10% of window size): _elen = total length of exonic DNA with window, standardize ...
... Only genes are taken into account that overlap by at least one base pair with window. Attributes are then calculated at exon level for each exon that fulfils the patch overlap definition (overlap >25% of exon length or >10% of window size): _elen = total length of exonic DNA with window, standardize ...
The vertebrate genome annotation (Vega) database
... about/gene_and_transcript_types.html. Generating the database for the Vega website As mentioned in Ashurst et al. (2), the data released via the Vega website is produced by merging two in-house databases at the Sanger Institute: the pipeline database containing the genome assembly and alignments of ...
... about/gene_and_transcript_types.html. Generating the database for the Vega website As mentioned in Ashurst et al. (2), the data released via the Vega website is produced by merging two in-house databases at the Sanger Institute: the pipeline database containing the genome assembly and alignments of ...
Concept_Paper
... develop and test technology to facilitate the cloning and sequencing of larger AT-rich-DNA genomes. c) Annotation of the Tetrahymena genomic information. The value of the Tetrahymena genomic sequence will be greatly enhanced by its high quality annotation, which will be done according to the followi ...
... develop and test technology to facilitate the cloning and sequencing of larger AT-rich-DNA genomes. c) Annotation of the Tetrahymena genomic information. The value of the Tetrahymena genomic sequence will be greatly enhanced by its high quality annotation, which will be done according to the followi ...
DNA Mutation and Repair
... DNA Mutation and Repair • Spontaneous mutations • DNA polymerase has a proofreading activity that normally keeps mutation rates low but accidents happen and • Some types of mutation are invisible to the polymerase • Strand slippage is common in repetitive regions of the genome • DNA forms a tempora ...
... DNA Mutation and Repair • Spontaneous mutations • DNA polymerase has a proofreading activity that normally keeps mutation rates low but accidents happen and • Some types of mutation are invisible to the polymerase • Strand slippage is common in repetitive regions of the genome • DNA forms a tempora ...
Sequences of flavivirus-related RNA viruses persist in DNA form
... to amplify the NS3 region of flaviviruses and a direct PCR protocol (without a reverse transcription step), we obtained repeatedly positive amplification results from DNA extracts of uninfected cultured C6/36 Aedes albopictus cells. Negative results were constantly obtained in similar conditions usi ...
... to amplify the NS3 region of flaviviruses and a direct PCR protocol (without a reverse transcription step), we obtained repeatedly positive amplification results from DNA extracts of uninfected cultured C6/36 Aedes albopictus cells. Negative results were constantly obtained in similar conditions usi ...
DNA Sequence Capture and Enrichment by Microarray Followed by
... Data Supplement). In addition, the number of the inserted-sequence reads (coverage) is low, which further challenges the detection of the inserted Alu sequence. We found 16 reads of the inserted alleles and 32 reads of wild-type alleles that crossed the insertion boundary. Although the inserted Alu ...
... Data Supplement). In addition, the number of the inserted-sequence reads (coverage) is low, which further challenges the detection of the inserted Alu sequence. We found 16 reads of the inserted alleles and 32 reads of wild-type alleles that crossed the insertion boundary. Although the inserted Alu ...
Methylation Dynamics in the Early Mammalian Embryo - Beck-Shop
... fertilization in the mouse, rat, pig, bovine, and human zygote, whereas the maternal genome is passively demethylated by a replication-dependent mechanism after the two-cell embryo stage. These genome-wide demethylation waves may have a role in reprogramming of the genetically inactive sperm and egg ...
... fertilization in the mouse, rat, pig, bovine, and human zygote, whereas the maternal genome is passively demethylated by a replication-dependent mechanism after the two-cell embryo stage. These genome-wide demethylation waves may have a role in reprogramming of the genetically inactive sperm and egg ...
Methylation Dynamics in the Early Mammalian Embryo: Implications
... fertilization in the mouse, rat, pig, bovine, and human zygote, whereas the maternal genome is passively demethylated by a replication-dependent mechanism after the two-cell embryo stage. These genome-wide demethylation waves may have a role in reprogramming of the genetically inactive sperm and egg ...
... fertilization in the mouse, rat, pig, bovine, and human zygote, whereas the maternal genome is passively demethylated by a replication-dependent mechanism after the two-cell embryo stage. These genome-wide demethylation waves may have a role in reprogramming of the genetically inactive sperm and egg ...
Comparative Genomics of Microbes
... – Base to base alignment – Highlights the exact matches and differences in the genomes – Locates ...
... – Base to base alignment – Highlights the exact matches and differences in the genomes – Locates ...
human endogenous retroviral LTR
... domestication of exogenous retroviruses that have been integrated into the germ line. The whole genome mapping of such elements in various species could reveal differences in positions of the retroviral integration and suggest possible roles of these differences in speciation. Here, we describe the ...
... domestication of exogenous retroviruses that have been integrated into the germ line. The whole genome mapping of such elements in various species could reveal differences in positions of the retroviral integration and suggest possible roles of these differences in speciation. Here, we describe the ...