Question

In: Biology

One difficulty in extracting sequencing reads that correspond to mitochondrial DNA from mixed fragments of nuclear...

One difficulty in extracting sequencing reads that correspond to mitochondrial DNA from mixed fragments of nuclear and mitochondrial DNA is the nuclear genome contains segments homologous to regions of the mitochondrial genome called "numts." Mammalian genomes contain 50-450 kb of numts (the human genome contains 1005 numts, averaging 446 bp).

Estimate the fraction of reads from fragments of mammoth DNA that are likely to be numts. The mammoth genome is approximately 4.7x10^9 bases in length.

Solutions

Expert Solution

Background Next generation ultra-sequencing technologies are starting to produce extensive quantities of data from entire human genome or exome sequences, and therefore new software is needed to present and analyse this vast amount of information. The 1000 Genomes project has recently released raw data for 629 complete genomes representing several human populations through their Phase I interim analysis and, although there are certain public tools available that allow exploration of these genomes, to date there is no tool that permits comprehensive population analysis of the variation catalogued by such data. Description We have developed a genetic variant site explorer able to retrieve data for Single Nucleotide Variation (SNVs), population by population, from entire genomes without compromising future scalability and agility. ENGINES (ENtire Genome INterface for Exploring SNVs) uses data from the 1000 Genomes Phase I to demonstrate its capacity to handle large amounts of genetic variation (>7.3 billion genotypes and 28 million SNVs), as well as deriving summary statistics of interest for medical and population genetics applications. The whole dataset is pre-processed and summarized into a data mart accessible through a web interface. The query system allows the combination and comparison of each available population sample, while searching by rs-number list, chromosome region, or genes of interest. Frequency and FST filters are available to further refine queries, while results can be visually compared with other large-scale Single Nucleotide Polymorphism (SNP) repositories such as HapMap or Perlegen. Conclusions ENGINES is capable of accessing large-scale variation data repositories in a fast and comprehensive manner. It allows quick browsing of whole genome variation, while providing statistical information for each variant site such as allele frequency, heterozygosity or FST values for genetic differentiation.


Related Solutions

Which type of enzyme is routinely used in biotechnology to cut DNA into fragments? Nuclear transplantation...
Which type of enzyme is routinely used in biotechnology to cut DNA into fragments? Nuclear transplantation (somatic cell nuclear transfer) is a technique that requires multiple steps. Which of the following steps is nota part of this technique? a. production of an enucleated egg (egg with the nucleus removed) b. de-differentiated (re-programmed) somatic cell c. fusion of a sperm cell with an egg cell d. fusion of a de-differentiated somatic cell with an enucleated egg
One thousand bases of quail mitochondrial DNA were downloaded to Geneious from the GenBank database. PCR...
One thousand bases of quail mitochondrial DNA were downloaded to Geneious from the GenBank database. PCR primers were designed to amplify a conserved region from this sequence. Each primer was 20 bases long, and the 5` end of the forward primer (F) and reverse primer (R) starts from base position 33 and 865, respectively. A PCR master mixture for 23 reactions to analyse different bird samples was prepared.                             Fill in the necessary information for the master mix in the following...
Which ONE sequence of events is correct in 454 sequencing? a. DNA extraction, amplification of exons,...
Which ONE sequence of events is correct in 454 sequencing? a. DNA extraction, amplification of exons, library preparation, sequencing, analysis of results. b. DNA extraction, amplification of exons, sequencing, library preparation, analysis of results. c. DNA extraction, sequencing, amplification of exons, , library preparation, analysis of results.
6) Why is it that only maternal mitochondrial DNA passes on from parent to offspring? (10...
6) Why is it that only maternal mitochondrial DNA passes on from parent to offspring? (10 pts) Assume the following for questions 7 & 8. Show work via Punnett squares a) Handedness is determined via maternal effect. b) Left handedness is recessive. c) Right handedness is dominant. 7) If your grandmother had the homozygous recessive trait and your grandfather was homozygous dominant what was your mother’s genotype and phenotype? (10pts) 8) Your father is heterozygous. What is your genotype and...
Why does DNA sequencing reaction use one primer and PCR use two primers?
Why does DNA sequencing reaction use one primer and PCR use two primers?
Java: create a program that reads in a piece of DNA sequence from a sequence file...
Java: create a program that reads in a piece of DNA sequence from a sequence file (dna.seq) (alternatively you can use the getRandomSeq(long) method of the RandomSeq class to generate a piece of DNA sequence), and then print out all the codons in three forward reading frames. Design a method called codon() that can be used to find all the codons from three reading frames. The method will take in an argument, the reading frame (1, 2, or 3), and...
Recent advances in molecular techniques have allowed scientists to successfully extract proteins and DNA fragments from...
Recent advances in molecular techniques have allowed scientists to successfully extract proteins and DNA fragments from extinct animals found in museum collections or the recent fossil record. In the near future, it may be possible to clone previously extinct organisms such as mammoths. What are your opinions on cloning extinct species?
Besides adding more data, why would researchers sequence several genres from the nuclear and mitochondrial genomes,...
Besides adding more data, why would researchers sequence several genres from the nuclear and mitochondrial genomes, as opposed to using just one gene to generate their phylogenetic hypothesis?
Recent advances in paleogenomics (the recovery and sequencing of DNA from remains up to about 80,000–100,000 years old)
Recent advances in paleogenomics (the recovery and sequencing of DNA from remains up to about 80,000–100,000 years old) have allowed geneticists to test a hypothesis long proposed by paleoanthropologists: that humans (Homo sapiens) interbred with other hominin species, such as Neanderthals (Homo neanderthalensis), that some human groups encountered as they migrated out of Africa. Early work in paleogenomics focused on mtDNA, and more recent work has assembled a complete autosomal genome sequence for Neanderthals. Surprisingly, paleogenomics has also recently identified...
Implement a function that reads numbers in from a file with one number per line and...
Implement a function that reads numbers in from a file with one number per line and outputs all the possible sums that can be formed by subsets of the numbers. For instance, if the numbers in the file are 1 2 4, then the output would be 0, 1, 2, 4, 3, 5, 6, 7. Note that 0 is in the output because it uses none of the numbers, while 7 is the sum of all of the numbers. //...
ADVERTISEMENT
ADVERTISEMENT
ADVERTISEMENT