Genomic Sequencing
Genomic Sequencing - Related Videos
12:36
Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA
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Cited by 2 •
2011
We present a public computational web site for the analysis of genomic sequences. It detects DNA sequence patterns with various non-random nucleotide compositions. This resource also generates randomized sequences with diverse levels of complexity.
14:06
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Cited by 10 •
2012
Pooled DNA sequencing is a fast and cost-effective strategy to detect rare variants associated with complex phenotypes in large cohorts. Here we describe the computational analysis of pooled, next-generation sequencing of 32 cancer-related genes using the SPLINTER software package. This method is scalable, and applicable to any phenotype of interest.
10:34
Ultra-long Read Sequencing for Whole Genomic DNA Analysis
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Cited by 28 •
2019
Long-read sequences greatly facilitate the assembly of complex genomes and characterization of structural variation. We describe a method to generate ultra-long sequences by nanopore-based sequencing platforms. The approach adopts an optimized DNA extraction followed by modified library preparations to generate hundreds of kilobase reads with moderate coverage from human cells.
09:31
Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
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Cited by 56 •
2016
We describe a protocol for amplifying retroviral integration sites from the genomic DNA of infected cells, sequencing the amplified virus-host junctions, and then mapping these sequences to a reference genome. We also describe techniques to quantify the distribution of integration sites relative to various genomic annotations using BEDTools.
09:40
Novel Sequence Discovery by Subtractive Genomics
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Cited by 8 •
2019
The purpose of this protocol is to use a combination of computational and bench research to find novel sequences that cannot be easily separated from a co-purifying sequence, which may be only partially known.
FAQs
These approaches produce millions of sequence reads, each representing information from portions of an organism’s DNA. Sequencing-by-synthesis records nucleotide incorporation during the creation of a complementary strand, whereas nanopore detection identifies DNA as it passes through a nanopore. The resulting reads are processed computationally so researchers can build and examine a broader representation of the genome.
Individual sequence reads provide only partial views of the DNA, so computational assembly combines them into a more continuous genomic representation. Comparison then places that information alongside other genomes or reference sequences. Together, these steps help researchers identify differences, examine shared features, and interpret genomic patterns rather than treating each read as an isolated observation.
Genomic sequencing can reveal genetic variants, support investigations of gene function, and show how genomes change over evolutionary time. It also helps researchers examine how genetic differences may relate to traits, disease, or responses to environmental conditions. These capabilities make the approach useful for studying both the structure of genetic information and its biological significance.
A typical workflow begins with DNA extraction and preparation, followed by generation of sequence reads using a method such as sequencing-by-synthesis or nanopore detection. Computational tools then assemble and compare the reads. The final analysis depends on the biological question, such as identifying variants, examining gene function, studying evolution, or characterizing a pathogen.
Researchers can apply genomic sequencing when they need to compare genetic information among organisms, populations, or related biological samples. Comparative genomics uses these data to examine similarities and differences, while population studies investigate patterns of genetic variation. Such analyses can provide evidence for evolutionary relationships and help connect genomic differences with biological traits or environmental responses.
For pathogen research, sequencing provides genomic information that can be examined and compared across samples. This supports characterization by revealing genetic variation and enabling relationships among pathogen genomes to be investigated. In the broader biological context, these analyses help researchers study how genomic differences may relate to traits, disease, and responses to environmental conditions.