Examples of shotgun sequencing in the following topics:
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- The strategies used for sequencing genomes include the Sanger method, shotgun sequencing, pairwise end, and next-generation sequencing.
- In the shotgun sequencing method, several copies of a DNA fragment are cut randomly into many smaller pieces (somewhat like what happens to a round shot cartridge when fired from a shotgun).
- This is the principle behind reconstructing entire DNA sequences using shotgun sequencing.
- Originally, shotgun sequencing only analyzed one end of each fragment for overlaps.
- Compare the different strategies used for whole-genome sequencing: Sanger method, shotgun sequencing, pairwise-end sequencing, and next-generation sequencing
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- These advances have allowed the adaptation of shotgun sequencing to metagenomic samples .
- The approach, used to sequence many cultured microorganisms and the human genome, randomly shears DNA, sequences many short sequences, and reconstructs them into a consensus sequence.
- Shotgun sequencing and screens of clone libraries reveal genes present in environmental samples.
- This was further followed by high-throughput sequencing which did the same process as the shotgun sequencing but at a much bigger scale in terms of the amount of DNA that could sequenced from one sample.
- (A) sampling from habitat; (B) filtering particles, typically by size; (C) Lysis and DNA extraction; (D) cloning and library construction; (E) sequencing the clones; (F) sequence assembly into contigs and scaffolds
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- Recent studies use "shotgun" Sanger sequencing or massively parallel pyrosequencing to get largely unbiased samples of all genes from all the members of the sampled communities.
- Advances in bioinformatics, refinements of DNA amplification, and the proliferation of computational power have greatly aided the analysis of DNA sequences recovered from environmental samples, This allows the adaptation of shotgun sequencing to metagenomic samples.
- Shotgun sequencing and screens of clone libraries reveal genes present in environmental samples.
- Shotgun metagenomics is also capable of sequencing nearly complete microbial genomes directly from the environment.
- On the other hand, the random nature of shotgun sequencing ensures that many of these organisms, which would otherwise go unnoticed using traditional culturing techniques, will be represented by at least some small sequence segments.
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- Sanger sequence can only produce several hundred nucleotides of sequence per reaction.
- Most next-generation sequencing techniques generate even smaller blocks of sequence.
- Most genomic sequencing projects today make use of an approach called whole genome shotgun sequencing.
- Whole genome shotgun sequencing involves isolating many copies of the chromosomal DNA of interest.
- In shotgun sequencing, multiple copies of the same chromosome are isolated and then fragmented in random locations.
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- There are 32 microbial genomes sequenced to date and published (25 domain Bacteria, 5 Domain Archaea, 1 domain Eukarya).
- There are two main approaches to sequencing microbial genomes – the ordered clone approach and direct shotgun sequencing both require large and small insert genomic DNA libraries in order to be effective.
- PCR products of every gene from a complete genome sequence are bound in a high-density array on a glass slide.
- Mutation is random, undirected, heritable variation caused by alteration in nucleotide sequence at some point of DNA.
- Summarize the techniques used to study genomes: PFGE. ordered clone approach, direct shotgun sequencing and microarray hybridization
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- The first genome to be completely sequenced was of a bacterial virus, the bacteriophage fx174 (5368 base pairs).
- This was accomplished by Fred Sanger using shotgun sequencing.
- Several other organelle and viral genomes were later sequenced.
- Having entire genomes sequenced aids these research efforts.
- The process of attaching biological information to gene sequences is called genome annotation.
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- Metagenomic sequencing is particularly useful in the study of viral communities.
- In 2002, Mya Breitbart, Forest Rohwer, and colleagues used environmental shotgun sequencing to show that 200 liters of seawater contains over 5,000 different viruses.
- (A) sampling from habitat; (B) filtering particles, typically by size; (C) Lysis and DNA extraction; (D) cloning and library construction; (E) sequencing the clones; (F) sequence assembly into contigs and scaffolds
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- A sequence is an ordered list of objects (or events).
- Also, the sequence $(1, 1, 2, 3, 5, 8)$, which contains the number $1$ at two different positions, is a valid sequence.
- Sequences can be finite, as in this example, or infinite, such as the sequence of all even positive integers $(2, 4, 6, \cdots)$.
- Finite sequences are sometimes known as strings or words, and infinite sequences as streams.
- The empty sequence $( \quad )$ is included in most notions of sequence, but may be excluded depending on the context.
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- An arithmetic sequence is a sequence of numbers in which the difference between the consecutive terms is constant.
- An arithmetic progression, or arithmetic sequence, is a sequence of numbers such that the difference between the consecutive terms is constant.
- For instance, the sequence $5, 7, 9, 11, 13, \cdots$ is an arithmetic sequence with common difference of $2$.
- The behavior of the arithmetic sequence depends on the common difference $d$.
- Calculate the nth term of an arithmetic sequence and describe the properties of arithmetic sequences
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- In a shotgun wedding, a marriage between two people is forced because of an unplanned pregnancy.
- As the stigma associated with out-of-wedlock births has faded over the years, and the number of such births has increased, shotgun weddings have become less common.
- Fewer people perceive shotgun weddings to be necessary in order to support the woman and the child.