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Physical genome maps:Mapping by fingerprinting

and anchoring

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Gene Mapping Similar to geographical maps , maps of

target DNA molecule gives location of

landmarksTwo types of gene mapping

Genetic mapping: statistical analysis of

inheritance pattern Physical mapping: physical and biochemical

experiments on DNA sequence

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Physical maps Physical maps include maps that provide

directly measured distances between

genomic elements or that order cloned

DNA fragments known to contain specific

genomic element.

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Types of physical Maps STS content Map

Clone based Maps

Radiation hybrid Maps

Sequence based Maps

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STS content Maps Particularly for compact genomes

This technique can resolve regions muchlarger than 1 Mb

Advantage of using convenient PCR

based positional markers. STS marker are assayed by PCR or

hybridization against a set or array of largeinsert clones

STS content mapping technique builds aseries of contigs (overlapping clusters ofclones joined together by shared STSs)

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Clone based maps

This technique rely on other than STS

content to determine the adjacency of

clones Fingerprinting is used commonly by

sequencing centers to assemble and BAC

and PAC contigs before clones are chosen

for sequencing

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Radiation hybrid maps : RH mapping is similar to linkage mapping

except that in RH breaks are induced by

the application of lethal doses of radiation Resolution of maps is proportional to the

amount of irradiation to which the donor cell-line was exposed

RH Map distances are directoryproportional to Physical distance

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Sequences Based Maps Complete genomic sequence available for

number of species are excellent source for

map information NCBI blast and e PCR are powerful tool

for finding marker sequence links

NCBI map Viewer helps to visualize the

maps and other sequence information ofdifferent species

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Mapping by fingerprinting

The idea in mapping by random clone overlap isthat clones are chosen at random

Fingerprint involves digesting the cloned DNAwith restriction enzymes

When two clones have enough fingerprint incommon , they are declared to overlap.

Clone that overlap are said to form Islands

At the beginning of mapping process , there aremany isolated clones which we refer to asSingleton Islands

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Mapping by Anchoring

There are alternate methods of physical mapping

Linking random clones by a technique, we will callanchoring

The new feature is a random genomic library of socalled Anchors

The anchors library contains a very smallgenomic inserts that uniquely identify a genomic

location which we point in the genome Anchoring involves determining which clones

contain a given anchor

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Two anchored Islands

Seven Clones

Three AnchorsThree singleton Unanchored islands

One singleton islands

One islands of three clones and two anchors

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Web resources UCSC genome browser :

To visualize both fingerprinting and STC data inhuman and other organism

WUGSC( Washington universitys Genomesequencing center)

BCGSC (British columbia genomic sequencecenter )

NCBI Map Viewer

Oakridge national Laboratorys Genome channelweb

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Other resources:

GDB (genome data base )

e genome

LDB 2000(hosted by university ofSouthampton )

Gene Cards

Gene Loc euGene

Ace view

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Softwares for physical mapping IMAGE (fingerprinting data)

FPC (fingerprinting data )

Both are available from Sanger Institute