Introduction Definition History Genes & genomes Mapping techniques – 1) genetic mapping 2) physical mapping Genomic databases Tools Human genome project Conclusion References

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/