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Published in Splinter Robert, Illustrated Encyclopedia of Applied and Engineering Physics, 2017
[biomedical, computational, theoretical] A comprehensive breakdown of the inherited information-bearing genetic material residing in the chromosomes (and hence dna) of an organism’s (i.e., genome). DNA is a biopolymer consisting of four nucleotide constituents: A (adenine), C (cytosine), G (guanine), and T (thymine). The study includes the analysis of the full complement of signaling codes that regulate the gene expression. Genomics focuses on species, not on individuals. The name originates from a journal title introduced in 1986 that publishes work related to gene sequencing, mapping and their activities. The information in the chromosomes is digital, consisting of DNA strings whose order provides information in 0s and 1s. Genomics is hence an information science. The study requires the establishment of a “reference genome” for a species of interest to provide a basis for the analysis of the global genomic composition and associated expressions. The most comprehensive DNA sequence-based investigation is the Human Genome Project.
Next generation sequencing for pandemic preparedness
Published in Indian Chemical Engineer, 2020
Genome sequencing helps identify variants compared to the reference genome. When multitude of samples are sequenced the differential frequency of mutations across geographical locations helps correlate with symptom diversity and clinical outcome. It also provides basal data towards calculating virus mutation rate and its plausible association with mortality. The variant and invariant regions in the pathogen genome vis-a-vis functional domains are also important for prioritising drug and vaccine targets. Genome sequencing is also an important tool towards understanding genetic epidemiology of the SARS-CoV-2 footprint in India as well as globally.
Maximum Exact Matches for High Throughput Genome Subsequence Assembly
Published in IETE Journal of Research, 2022
This work proposes an effective subsequence based matching technique to aid in the process of DNA sequencing. A reference genome is used as the base for the sequencing process. The DNA fragments are grouped into subsets of fragments and a perfect match is identified on the reference genome. The matching indices are noted and a complete matching is performed only on the specific indices based on the Hamming Distance levels. This enables a huge reduction in the search process. Further, the entire matching process is parallelized resulting in a fast and effective sequencing model.