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Impact of Whole Genome SequencingBY: anisha kathpalia | Category: Bioinformatics | Submitted: 2011-06-30 23:20:20
Article Summary: "Whole genome sequencing is determining the sequence of the entire genome of an organism.Different organism's genomes have been sequenced including that of human.Different bionformatics tools & databases are used for browsing & analysing the genome sequences.This whole genome sequence has helped in different aspects of biotechnol.."
Complete genome sequencing or whole genome sequencing, is a process of determining the complete DNA sequence of an organism's genome i.e the sequence of A.T,G,C nucleiotides which are present in coding as well as non coding regions. There are large number of genomes that have been sequenced till date. These include Haemophilus influenza & Mycoplasma genitalium (1995), E. coli & S. Cerevisiae(1997), Drosophila & Arabidopsis thaliana (2000 ) ,Human genome (2003).
There are essentially two techniques for sequencing a complete genome. These are BAC-to-BAC method (the hierarchial shotgun sequencing method) & the Shotgun sequencing
Since the genome of an organism contains large & immense amount of DNA, maps are needed to order the clones and locate the genes for genetic disorders. These maps require certain landmarks ; out of which the most common landmark is STS (sequence-tagged site).There are two types of maps:
Genetic maps: Gives information about the genetic nature of the genome & therefore it is the measure of the genetic recombination in a particular chromosomal region. These are constructed by evaluating the genotypes of a set of markers in groups of related individuals. This mapping data can be analysed by software like MapMaker which help in constructing genetic maps by taking into account the frequency of alleles at any two markers which are inherited together
Physical maps give the physical distance i.e. DNA-base-pair distances from one landmark to another. The first step in constructing a physical map consists of describing the genome as an ordered set of restriction endonuclease segments.
Sequence tagged site (STS) mapping is an important physical mapping technique.STS is a unique DNA sequence that is a few hundred base pair long & is found in only one place in the genome There are 3 types of physical maps. These are:Sequence maps, RH maps ,Cytogenetic map or chromosomal map
NCBI's MapViewer is a widely used bioinformatics tool for integrating physical & genetic maps. MapViewer can display simultaneously up to seven maps, which are selected from a large set of maps and allows the user to access detailed information for a selected map region.It currently has map of over 106 species
Bioinformatics in genome sequencing : There are different databases & tools available in bioinformatics which provide us the information about the genome sequence. There are different genome sequence databases freely available to public.These are:
NCBI ,UCSC's Genome Browser & Ensembl
These are the important resources containing a large amount of useful genome sequence data of various species.
There are different softwares available for analysis of the genomic sequences available in the databases. These softwares help in understanding the different sequences for identification of different introns , exons ,promoters etc. These include: GeneScan,GLIMMER(Gene Locator and Interpolated Markov ModelER), GeneMark , FGENE, FEX , FGENESP etc.
Applications of complete genome sequences
There are numerous applications of these available complete genome sequences of various organisms. These applications cover various aspects of biotechnology like:
Disease Diagnosis- Genome-wide studies is a powerful approach for identification of genes involved in common human diseases .These whole genome analysis also helps in solving various genetic problems that are difficult to be tackled using conventional approaches like identification of molecular basis of multigenic and complex traits.
Crop Improvement -Knowing the whole genome sequence for different plant species has led to development of molecular markers and for identification of genes which are of agronomic importance. This can speed up the breeding process & may give rise to improved varieties with improved yield & quality.
Molecular Medicine- High throughput genome sequencing has also led to pharacogenomics "custom drugs". It has led to personalised medicines for individual human beings as different individuals show a different response to a particular medicine.
Forensics -An organism can be identified accurately by its DNA sequence.So the genome sequences available for different organisms has helped greatly in the field of forensics for identification of suspects whose DNA may match evidence left at the crime scenes & for determining parentage & other family relationships. This has solved many criminal cases & has led to identification of human remains.
Cancer research-With development of projects like cancer genome project every cancer can now be classified & the different genes involved in different cancers have been identified. Whole genome sequencing has enabled to map a person's DNA & design customized treatments for different types of cancers which may help in fighting cancer more effectively than the conventional treatments used as for almost all the cancers.
About Author / Additional Info:
A Mtech bioinformatics student from Delhi.I just wanted to share some basic knowledge about the new emerging field of bio-informatics.
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