Shotgun sequencing

Whole genome shotgun sequencing versus Hierarchical shotgun sequencing

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Tiling path

Shotgun sequencing is a method used for DNA sequencing. It is a technique in which DNA is broken up randomly into numerous small segments, which are then sequenced individually. The sequences of these fragments are then reassembled into a continuous sequence by using computer algorithms, based on overlapping regions of the fragments.

History

Shotgun sequencing was first developed in the 1970s and became more widely used in the 1990s with the advent of high-throughput sequencing technologies. It was notably used in the Human Genome Project to sequence the human genome.

Methodology

The process of shotgun sequencing involves several key steps:

1. Fragmentation: The DNA is randomly fragmented into smaller pieces.
2. Sequencing: Each fragment is sequenced using Sanger sequencing or other sequencing technologies.
3. Assembly: The sequences of the fragments are assembled into a continuous sequence using computational methods. This involves finding overlapping regions between fragments and aligning them to reconstruct the original DNA sequence.

Applications

Shotgun sequencing is widely used in various fields of genomics and molecular biology. Some of its applications include:

• Genome sequencing: It is used to sequence the genomes of various organisms.
• Metagenomics: Shotgun sequencing is used to analyze the genetic material from environmental samples, allowing the study of microbial communities.
• Comparative genomics: It helps in comparing the genomes of different species to understand evolutionary relationships.

Advantages and Disadvantages

Advantages

• Speed: Shotgun sequencing can be faster than other sequencing methods because it allows for parallel processing of multiple fragments.
• Cost-effective: It can be more cost-effective, especially with the use of high-throughput sequencing technologies.

Disadvantages

• Complexity: The assembly process can be computationally intensive and complex, especially for large genomes with repetitive sequences.
• Error-prone: Errors can occur during the assembly process, leading to gaps or incorrect sequences.

See also

• DNA sequencing
• Human Genome Project
• High-throughput sequencing
• Sanger sequencing
• Genomics
• Metagenomics
• Comparative genomics