Genomic mapping by kk sahu
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The document discusses genome mapping, defining it as the process of creating genetic maps that assign DNA fragments to chromosomes, assisting scientists in navigating the genome. It outlines the history of genome mapping, various techniques such as genetic and physical mapping, and the tools developed for analyzing genomic data, including databases and software programs. Additionally, it highlights the Human Genome Project's objectives and its significance in advancing medical research and biotechnology.
Genomic mapping by kk sahu
- 1. Genomicmapping By KAUSHAL KUMAR SAHU Assistant Professor (Ad Hoc) Department of Biotechnology Govt. Digvijay Autonomous P. G. College Raj-Nandgaon ( C. G. )
- 2. Synopsis Introduction Definition History Genes & genomes Mapping techniques – 1) genetic mapping 2) physical mapping Genomic databases Tools Human genome project Conclusion References
- 3. Introduction Genome mapping, also called gene mapping, is the creation of a genetic map assigning DNA fragments to chromosomes. A genome map helps scientists navigate around the genome. Like road maps and other familiar maps, a genome map is a set of landmarks that tells people where they are, and helps them get where they want to go. In most living things, the genome is made of a chemical called DNA. Each one of earth's species has its own distinctive genome.
- 4. Definition The technique of locating the gene is called genome mapping. It describes the order of genes or other markers and the spacing between them on each chromosome. The first genome of a living organism was Haemophilus influenza in 1995.
- 5. History 1953 – Watson-crick structure of DNA published. 1975 – F. Sanger and independently A. Maxam & W.Gilbert, develop methods for sequencing DNA. 1981 – Human mitochondrial DNA sequenced ; 16,569 bp. 1995 – First complete sequence of a bacterial genome, Haemophilus influenza, by TIGR. 1996 – Completion of yeast genome, first eukaryotic genome sequence. 1 dec. 1999 – Sequence of first complete human chromosome published.
- 6. Genes & Genomes Genes can be defined as the “functional part of DNA”. It is a small defined section of the entire genome sequences and each gene has a specific unique purpose. Genome can be defined as the “total genetic constituent of an organism”.
- 7. Fig. genome sizes of different species
- 8. Mapping techniques Two types of techniques are their :- 1 )Genetic mapping 2) Physical mapping Genetic mapping Genetic mapping is based on the use of genetic techniques to construct maps showing the positions of genes and other sequence features on a genome. The first genetic maps, constructed in the early decades of the 20th century for organisms such as the fruit fly, used genes as markers.
- 9. DNA markers for genetic mapping Genes are very useful markers but they are by no means ideal. One problem, especially with larger genomes such as those of vertebrates and flowering plants, is that a map based entirely on genes is not very detailed. We need other types of marker. Mapped features that are not genes are called DNA markers There are three types of DNA sequence feature that satisfy this requirement: restriction fragment length polymorphisms (RFLPs), simple sequence length polymorphisms (SSLPs), and single nucleotide polymorphisms (SNPs).
- 10. RFLPs - RFLPs were the first type of DNA marker to be studied. RFLPs can be used to measure recombination rates which can lead to a genetic map with the distance between RFLP loci measured in centi Morgans. Analysis of RFLP variation in genomes was a vital tool in genome mapping and genetic disease analysis. There are thought to be about 105 RFLPs in the human genome, but of course for each RFLP there can only be two alleles. SSLPs - SSLPs are arrays of repeat sequences that display length variations, different alleles containing different numbers of repeat units. Unlike RFLPs, SSLPs can be multi-allelic.
- 11. SNPs - These are positions in a genome where some individuals have one nucleotide (e.g. a G) and others have a different nucleotide (e.g. a C). There are vast numbers of SNPs in every genome. In the human genome there are at least 1.42 million SNPs.
- 12. Physical mapping Physical mapping uses molecular biology techniques to examine DNA molecules directly in order to construct maps showing the positions of sequence features, including genes.
- 13. Physical mapping techniques a)Fluorescence in situ hybridization (FISH) In situ hybridization is a version of hybridization analysis in which an intact chromosome is examined by probing it with a labeled DNA molecule. The position on the chromosome at which hybridization occurs provides information about the map location of the DNA sequence used as the probe.
- 14. b) Sequence tagged site (STS) mapping To generate a detailed physical map of a large genome we need, ideally, a high-resolution mapping procedure that is rapid and not technically demanding. At present the most powerful physical mapping technique, and the one that has been responsible for generation of the most detailed maps of large genomes, is STS mapping(olson et al). A STS is simply a short DNA sequence, generally between 100 and 500 bp in length.
- 15. Genomic databases •Genomes Server -this server gives access to a hundreds of complete genome sequences, including those from archaea, bacteria, eukaryota, organelles, plasmids and viruses. •Karyn's Genomes - contains general information about organisms whose genomes are completely sequenced. The main aim of the database is to provide a short and concise explanation as to why it is important to obtain these organisms genomic sequences. •FlyBase - the database for Drosophila melanogaster is one of the best- curated genetic databases.
- 16. •MGD- the 'Mouse Genome Database' is one of the most comprehensively curated genetic databases. •RGD- the 'Rat Genome Database' curates and integrates rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model for the study of human disease. •Plant databases- MaizeDB is the database for genetic data on maize. The 'Plant Genome Information Resource' (PGDIC) provides access to many different plant genome databases, including chlamydomonas, cotton, alfalfa, wheat, barley, rye, rice, millet, sorghum and species of solanaceae and trees. MENDEL is a plant-wide database for plant genes.
- 17. •GOLD – genome online database is a World Wide Web resource for comprehensive access to information regarding genome sequencing project.
- 18. •MBGD– microbial genome database is a database for comparative analysis of completely sequenced microbial genomes, the no. of which is now growing rapidly.
- 19. TOOLS The Bioinformatics tools are the software programs for the saving, retrieving and analysis of Biological data and extracting the information from them. This tool compares nucleotide or protein sequences to genomic sequence databases and calculates the statistical significance of matches. BLAST (BASIC LOCAL ALIGNMENT SEARCH TOOL) It is a program for sequence similarity searching developed at the NCBI. It identifies genes and genetic features.
- 20. FASTA (FAST-ALL) FASTA is a DNA and protein sequence alignment software package. It is used for a fast protein or fast nucleotide comparison. EMBOSS EMBOSS (The European Molecular Biology Open Software Suite) is a new, free open source software analysis package specially developed for the needs of the molecular biology user community. with in EMBOSS you will find around 100 programs (applications) for sequence alignment, database searching with sequence patterns, nucleotide sequence pattern analysis etc. http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/
- 21. Clustalw ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences, calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. RasMol It is a powerful research tool to display the structure of DNA, proteins, and smaller molecules. Protein Explorer, a derivative of RasMol, is an easier to use program.
- 22. SVA Sequence Variant Analyzer (SVA) is a tool developed to analyze genetic variants from whole-genome sequencing studies. Software: SequenceVariantAnalyzer URL: http://www.svaproject.org/
- 23. Human genome project The Human Genome Project (HGP) was a 13-year project coordinated by the U.S. Department of Energy and the National Institutes of Health. Project goals were- to identify all the approximately 20,000-25,000 genes in human DNA . determine the sequences of the 3 billion chemical base pairs that make up human DNA. store this information in databases,. improve tools for data analysis.
- 24. Conclusion Current & potential applications of genome research will address national needs in molecular medicine, waste control and environmental cleanup, biotechnology, energy sources, and risk assessment. The knowledge of genome mapping would lead to better medical management of the diseases and pharmaceuticals discovery.
- 25. References C.S.V. Murthy, Bioinformatics. First edition David W. Mount, Bioinformatics:sequence & genome analysis. 2nd edition B.D.Singh, Biotechnology. Expanding Horizons. 1st edition Websites- www.genomenewsnetwork.org www.ncbi.nlm.nih.gov www.genome.gov www.tigr.org/