Introduction to Genome Survey Sequencing
Genome survey sequences GSSs) are nucleotide sequences that are analogous to expressed sequence tags (ESTs) in bioinformatics and computational biology, with the exception that most of them are genomic rather than mRNA-derived.
Genome survey sequences are usually produced and presented to NCBI by labs that conduct genome sequencing, and they are utilized as a template for mapping and sequencing of genome size pieces involved in the conventional GenBank divisions, among other factors. due to their fragmentary nature, genomic survey sequences lack long-range continuity, making it more difficult to forecast gene and marker order. For example, detecting repetitive sequences in GSS info may not be feasible because the repetitive genome may be greater than the reads, making it hard to identify all the repeats.
Types of Data Present in GSS Division
The following data types are found in the GSS division:
1. Random "Single Pass Read" Genome Survey Sequences
Random "single-pass read" genome survey sequences are GSSs created by random selection along with a single pass read. On the rapid accumulation of genomic data, single-pass sequencing with reduced fidelity can be employed, but it has a lesser accuracy. It contains RAPD, RFLP, and AFLP, among other factors.
2. Cosmid/BAC/YAC End Sequences
Cosmid/BAC/YAC end sequences sequence the genome from the end side using Cosmid/Bacterial artificial chromosome/Yeast artificial chromosome. These sequences behave like low-copy plasmids, with only one copy per cell in some cases. They'll need a lot of E. coli culture to get enough chromosomes, so 2.5 - 5 liters might be a good amount.
3. Exon Trapped Genomic Sequences
Cosmid/BAC/YAC end sequences sequence the genome from the end side using Cosmid/Bacterial artificial chromosome/Yeast artificial chromosome. These sequences behave like low-copy plasmids, with only one copy per cell in some cases. They'll need a lot of E. coli culture to get enough chromosomes, so 2.5 - 5 liters might be a good amount. Exon can stay in mRNA during slicing, and the data carried by exon can be stored in the protein. Because DNA fragments can be implanted into sequences, if an
4. Alu PCR Sequences
In the mammalian genome, the Alu repetitive element is a part of the Short Interspersed Elements (SINE) family. Alu PCR is a method for "DNA fingerprinting." This method is quick and simple to implement. It was discovered through the examination of many genomic loci flanked by Alu repetitive elements, which are non-autonomous retrotransposons found in large numbers in primate genomes. The Alu element can be utilized for genome fingerprinting using PCR, also known as Alu PCR.
5. Transposon-Tagged Sequences
The most direct process of evaluating the purpose of a specific gene sequence is to substitute it or trigger a mutation and then evaluate the results and effects. Gene replacement, sense, and antisense suppression, and insertional mutagenesis are three methods that have been established for this purpose. Among these techniques, insertional mutagenesis has proven to be extremely effective.
Applications of Genome Survey Sequencing
Because it is not reliant on mRNA, genome survey sequencing is the latest manner to map the genome sequences. GSS is frequently used on the first stage of genome sequencing in today's methods, which are mostly high-throughput shotgun techniques. GSSs, unlike ESTs, can offer an initial global perspective of a genome that contains both coding and non-coding DNA and involves repetitive sections of the genome. Because this information can influence the evaluation of sequence coverage, library quality, and the building process, GSS carries a crucial role in the early analysis of a sequencing project for the approximation of repetitive sequences.
GSS is also a good way to characterize genomes of similar species on a large scale and quickly, especially when there are few gene sequences or maps. With a poor coverage of GSS, comparative organisms can yield a lot of data about gene content and putative regulatory elements. It can evaluate the genes of similar species to determine whether the families are relatively expanded or contracted. Scientists can easily traverse the genome and classify the particular genomic section using more extensive sequencing when coupled with physical clone coverage.
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References
- Zhou XJ, Liu MX, Lu XY, et al. Genome survey sequencing and identification of genomic SSR markers for Rhododendron micranthum. Bioscience reports. 2020, 40(6).
- Adelyna MN, Jung H, Chand V, et al. A genome survey sequence (GSS) analysis and microsatellite marker development for Indian mackerel, Rastrelliger kanagurta, using Ion Torrent technology. Meta Gene. 2016, 10.
