Updated slides on graph algorithms for DNA sequencing
... Derive each consensus base by weighted voting Another approach based on finding a longest path in a DAG is given in the popular assembler Phrap ...
... Derive each consensus base by weighted voting Another approach based on finding a longest path in a DAG is given in the popular assembler Phrap ...
Wolbachia–host interactions: connecting phenotype to genotype
... crustaceans and most filarial nematode species [4–9], making it one of the most successful intracellular symbionts yet described. This success has been attributed to its ability to modify host reproductive biology in order to favour its own transovarial transmission. The most common reproductive phe ...
... crustaceans and most filarial nematode species [4–9], making it one of the most successful intracellular symbionts yet described. This success has been attributed to its ability to modify host reproductive biology in order to favour its own transovarial transmission. The most common reproductive phe ...
Whose Genetic Information Is It Anyway?
... 2 (July 14, 2000) (available in 2000 WL 17145183); see also William S. m0ug & Michael R. ...
... 2 (July 14, 2000) (available in 2000 WL 17145183); see also William S. m0ug & Michael R. ...
Pristionchus pacificus
... expected to be much older. However, as no fossil record exists for nematodes, no accurate numbers can be given. We are currently working on accurate estimates within the genus Pristionchus by using detailed molecular phylogenetics (W. Mayer and R. J. Sommer, ongoing studies). ...
... expected to be much older. However, as no fossil record exists for nematodes, no accurate numbers can be given. We are currently working on accurate estimates within the genus Pristionchus by using detailed molecular phylogenetics (W. Mayer and R. J. Sommer, ongoing studies). ...
Standards and guidelines for the interpretation of sequence
... that have developed variant classification guidelines for wellstudied genes in breast cancer, colon cancer, and cystic fibrosis and statistical analysis programs for quantitative evaluation of variants in select diseases.2–5 While those variant analysis guidelines are useful in a specific setting, i ...
... that have developed variant classification guidelines for wellstudied genes in breast cancer, colon cancer, and cystic fibrosis and statistical analysis programs for quantitative evaluation of variants in select diseases.2–5 While those variant analysis guidelines are useful in a specific setting, i ...
Ingenuity Variant Analysis
... mutation, but does not show the same single nucleotide base change. We only check exact nucleotides for SNVs, any insertions/deletions are by default checked only by coords. Base matching variants are more interesting than ones just overlapping, but one really has to look at each case. HGMD Disease: ...
... mutation, but does not show the same single nucleotide base change. We only check exact nucleotides for SNVs, any insertions/deletions are by default checked only by coords. Base matching variants are more interesting than ones just overlapping, but one really has to look at each case. HGMD Disease: ...
Folie 1 - NETTAB
... Hospital Bonn participated in the Boston Children’s Hospital’s CLARITY challenge. ...
... Hospital Bonn participated in the Boston Children’s Hospital’s CLARITY challenge. ...
CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI The
... The translocation junctions for long-range rearrangements had several notable features. Unlike control chromosomes, microhomology was observed at >50% of the junctions from the missegregated chromosomes, a higher frequency than expected by chance21 (Extended Data Fig. 7a). Microhomology could origin ...
... The translocation junctions for long-range rearrangements had several notable features. Unlike control chromosomes, microhomology was observed at >50% of the junctions from the missegregated chromosomes, a higher frequency than expected by chance21 (Extended Data Fig. 7a). Microhomology could origin ...
Rates of Spontaneous Mutation
... The data underlying this value are in Table 1 of Pathak and Temin (1990). That table described six mutations in the VP212-9 clone and added them to eight; in reality, there were seven mutations, which include F92 (described in their Table 2) (H. M. Temin, personal communication). The total of 37 mut ...
... The data underlying this value are in Table 1 of Pathak and Temin (1990). That table described six mutations in the VP212-9 clone and added them to eight; in reality, there were seven mutations, which include F92 (described in their Table 2) (H. M. Temin, personal communication). The total of 37 mut ...
Pathogen Genomics Into Practice
... methods, enabling outbreaks to be resolved or ruled out with greater speed, accuracy and confidence ...
... methods, enabling outbreaks to be resolved or ruled out with greater speed, accuracy and confidence ...
Polymorphisms in Multiple Genes Contribute to the
... direct-repeat recombination involving short homologous sequences (Gaillard and Bernardi 1979; Gaillard et al. 1980). However, neither the defects in mtDNA processing that lead to direct-repeat recombination nor the conditions that may determine its occurrence are known. Given the large number of gen ...
... direct-repeat recombination involving short homologous sequences (Gaillard and Bernardi 1979; Gaillard et al. 1980). However, neither the defects in mtDNA processing that lead to direct-repeat recombination nor the conditions that may determine its occurrence are known. Given the large number of gen ...
Specialized Transduction by Bacteriophage P22 in Salmonella typhimurium: Genetic and Physical Structure of the Transducing Genomes and the Prophage Attachment Site.
... P22pro-I and P22pro-3 are specialized transducing derivatives of phage P22 that carry the proA and proB genes of Salmonella typhimurium. These genes lie immediately adjacent to the prophage attachment site on the bacterial chromosome. By examining DNA heteroduplexes in the electron microscope, we fo ...
... P22pro-I and P22pro-3 are specialized transducing derivatives of phage P22 that carry the proA and proB genes of Salmonella typhimurium. These genes lie immediately adjacent to the prophage attachment site on the bacterial chromosome. By examining DNA heteroduplexes in the electron microscope, we fo ...
Sequence variation in the dihydrofolate reductase
... Dihydrofolate reductase-thymidylate synthase (DHFR-TS ) and trypanothione reductase (TR ) are important enzymes for the metabolism of protozoan parasites from the family Trypanosomatidae (e.g. Trypanosoma spp ., Leishmania spp. ) that are targets of current drug-design studies. Very limited informat ...
... Dihydrofolate reductase-thymidylate synthase (DHFR-TS ) and trypanothione reductase (TR ) are important enzymes for the metabolism of protozoan parasites from the family Trypanosomatidae (e.g. Trypanosoma spp ., Leishmania spp. ) that are targets of current drug-design studies. Very limited informat ...
Inference of homologous recombination in bacteria using whole
... In previous work, we developed a method to infer the clonal genealogy of a group of organisms, while simultaneously identifying for each branch of that genealogy the genomic locations where recombination occurred. The implementation of that method in software is called ClonalFrame [13]. ClonalFrame ...
... In previous work, we developed a method to infer the clonal genealogy of a group of organisms, while simultaneously identifying for each branch of that genealogy the genomic locations where recombination occurred. The implementation of that method in software is called ClonalFrame [13]. ClonalFrame ...
Complete comparative genomic analysis of two field isolates of
... also contains multiple deletions in the v90/4 genome. The largest deletion is a 1165 bp fragment that contains orf21 (bro-a) and a portion of orf20. An alignment of the v90/4 and v90/2 sequences around the junction regions of the 1165 bp deletion is shown in Fig. 3. The 1165 bp fragment contains a p ...
... also contains multiple deletions in the v90/4 genome. The largest deletion is a 1165 bp fragment that contains orf21 (bro-a) and a portion of orf20. An alignment of the v90/4 and v90/2 sequences around the junction regions of the 1165 bp deletion is shown in Fig. 3. The 1165 bp fragment contains a p ...
Direct and indirect consequences of meiotic recombination
... mismatches formed during homologous recombination. The second, which we term ‘hotspot drive’, results from the biased transmission of non-recombinogenic alleles over recombinogenic ones in hotspots of recombination [19]. The third, which we term ‘indel drive’, refers to the biased transmission of ei ...
... mismatches formed during homologous recombination. The second, which we term ‘hotspot drive’, results from the biased transmission of non-recombinogenic alleles over recombinogenic ones in hotspots of recombination [19]. The third, which we term ‘indel drive’, refers to the biased transmission of ei ...
Detecting copy number variants and runs of homozygosity on a
... or syndrome is a key objective in human genetics. Copy number variants (CNVs) and other forms of structural variation are important in understanding the underlying mechanisms to many common diseases. CNVs are defined as chromosomal segments, at least 1000 bases in length that vary in copy number (CN ...
... or syndrome is a key objective in human genetics. Copy number variants (CNVs) and other forms of structural variation are important in understanding the underlying mechanisms to many common diseases. CNVs are defined as chromosomal segments, at least 1000 bases in length that vary in copy number (CN ...
Biomart/ GENOME ALIGNMENT III
... aligning large genomic regions and subsequently sifting through massive amounts of data. In order to facilitate the discovery process without requiring biologists to download and install complex software, a number of web servers for alignment and analysis have been set up in recent years. These serv ...
... aligning large genomic regions and subsequently sifting through massive amounts of data. In order to facilitate the discovery process without requiring biologists to download and install complex software, a number of web servers for alignment and analysis have been set up in recent years. These serv ...
A High Density Integrated Genetic Linkage Map of Soybean and the
... be the most abundant source of DNA polymorphisms in soybean (Hyten et al., 2006; Zhu et al., 2003). Despite being the most common molecular marker in soybean, the SNP frequency is relatively low compared to other cultivated crop species (Hyten et al., 2006; Zhu et al., 2003). The relatively low sequ ...
... be the most abundant source of DNA polymorphisms in soybean (Hyten et al., 2006; Zhu et al., 2003). Despite being the most common molecular marker in soybean, the SNP frequency is relatively low compared to other cultivated crop species (Hyten et al., 2006; Zhu et al., 2003). The relatively low sequ ...
Assessment of the mosaic structure in the
... located about 300 bp upstream of the first EPIYA/T motif. They have shown that strains with an 18 bp or 39 bp deletion in the pre-EPIYA/T region possessed an EPIYA/T-D segment, whereas strains without any deletion commonly had an EPIYA/T-C segment [13]. In this study we used DNA isolated from 24 arc ...
... located about 300 bp upstream of the first EPIYA/T motif. They have shown that strains with an 18 bp or 39 bp deletion in the pre-EPIYA/T region possessed an EPIYA/T-D segment, whereas strains without any deletion commonly had an EPIYA/T-C segment [13]. In this study we used DNA isolated from 24 arc ...
Introduction - Stellenbosch University
... 8. thickEnd - The ending position at which the feature is drawn thickly (for example the stop ...
... 8. thickEnd - The ending position at which the feature is drawn thickly (for example the stop ...
A RARE KEL17/KEL(IVS3+1G>A) COMPOUND HETEROZYGOUS
... Background: The Kell blood group system includes some of the most immunogenic antigens among blood a a groups know. Among them Kell(KEL1), Kp (KEL3), and Js (KEL6) are well known. The antithetic antigens KEL11/17 further contribute to this list. However, KEL17 is considered as very rare, with an app ...
... Background: The Kell blood group system includes some of the most immunogenic antigens among blood a a groups know. Among them Kell(KEL1), Kp (KEL3), and Js (KEL6) are well known. The antithetic antigens KEL11/17 further contribute to this list. However, KEL17 is considered as very rare, with an app ...
De novo mutations in human genetic disease
... number of cell divisions in the male germline (compared with the female germline), during which replication mistakes can occur. Some gene mutations, however, show a paternal-age effect that is much stronger than expected and is driven by the mutation conferring a selective advantage during spermatog ...
... number of cell divisions in the male germline (compared with the female germline), during which replication mistakes can occur. Some gene mutations, however, show a paternal-age effect that is much stronger than expected and is driven by the mutation conferring a selective advantage during spermatog ...
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.