Physical genome maps: Mapping by fingerprinting and anchoring

Gene Mapping
Similar to geographical maps , maps of target DNA molecule gives location of landmarks Two types of gene mapping  Genetic mapping: statistical analysis of


inheritance pattern


Physical mapping:

physical experiments on DNA sequence

and

biochemical

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.

Types of physical Maps

   

STS content Map Clone based Maps Radiation hybrid Maps Sequence based Maps

 STS
   

content Maps

Particularly for compact genomes This technique can resolve regions much larger 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 large insert clones STS content mapping technique builds a series of contigs (overlapping clusters of clones joined together by shared STSs)

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

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 directory proportional to Physical distance

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 of different species

Mapping by fingerprinting
    

The idea in mapping by random clone overlap is that clones are chosen at random Fingerprint involves digesting the cloned DNA with restriction enzymes When two clones have enough fingerprint in common , they are declared to overlap. Clone that overlap are said to form Islands At the beginning of mapping process , there are many isolated clones which we refer to as Singleton Islands

Mapping by Anchoring
   

There are alternate methods of physical mapping Linking random clones by a technique, we will call anchoring The new feature is a random genomic library of so called Anchors The anchors library contains a very small genomic inserts that uniquely identify a genomic location which we point in the genome Anchoring involves determining which clones contain a given anchor

Two anchored Islands

Seven Clones Three Anchors Three singleton Unanchored islands One singleton islands One islands of three clones and two anchors

Web resources
UCSC genome browser : To visualize both fingerprinting and STC data in human and other organism  WUGSC( Washington universitys Genome sequencing center)  BCGSC (British columbia genomic sequence center )  NCBI Map Viewer  Oakridge national Laboratorys Genome channel web


Other resources:
      

GDB (genome data base ) e genome LDB 2000(hosted by university Southampton ) Gene Cards Gene Loc euGene Ace view

of

Softwares for physical mapping

  

IMAGE (fingerprinting data) FPC (fingerprinting data ) Both are available from Sanger Institute