SGD Help: Combined Physical and Genetic Maps
Contents
The Combined Physical and Genetic Map for an individual chromosome is
a side by side representation of the physical and genetic maps for the
chromosome. It contains genetically and/or physcially mapped ORFs.
The Combined Physical and Genetic Maps are derived from the systematic
genomic sequencing data and from data contained within SGD (Cherry JM,
Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles
L, Mortimer RK, Botstein D. Nature 387(6632S):67-73
(1997)), as well as data presented in earlier reviews (Mortimer and
Schild Microbiol. Rev. 44:519-571 (1980),
Microbiol. Rev. 49:181-213 (1985), Mortimer et al.,
Yeast 5:321-404 (1989), Mortimer et al., Yeast
8:817-902 (1992)). In the case where an ORF has been defined,
its standard gene name is indicated.
Information about the layout of the Combined
Physical and Genetic Map for an individual chromosome is given below.
- Physical and Genetic Map positions: The Physical Map is on
the left (in Kbp) and the Genetic Map is on the right (in cM).
Correspondingly, the Kbp scale is on the left side of the window and
the cM scale is on its right side.
- ORF Identification on the Physical Map: ORFs
are identified by blue (Crick strand) and red (Watson strand) bars on
the physical map. The ORF boxes on the left of the physical map line
are for ORFs which have been mapped physically, but not genetically
(i.e. gene B in the display). The boxes to the right of the physical
map line are for those ORFs which have been mapped both physically and
genetically (i.e. genes A and C in the display).
- ORF Labelling: All identified ORFs
are present as bars on the Combined Genetic and Physical Map. In the
case where an ORF has been defined, its primary gene name is present
on the map. ORFs without gene names are represented only by bars on
the map. In order to identify the ORF name for a bar which is not
labelled on the map, run the cursor over the bar and look at the
linking URL address at the bottom of the page.
- ORF Identification on the Genetic Map: ORFs
are identified on the genetic map by horizontal tick marks to the
right of the genetic map.
- Lines connecting the Physical and Genetic Maps: Lines
connect genetically mapped genes with their ORFs
on the physical map. In this case, the line extends from the top of
the ORF's colored box on the physical map to the corresponding tick
mark on the genetic map (see genes A and C for an example).
- Getting to the Locus window: The locus
entry can be found for any of the ORFs
or centromeres displayed by clicking on the desired ORF name, red or
blue bars, or the centromeres.
- Overlapping ORFs: In the case of overlapping ORFs,
the element at the bottom is shown to overlap the element at the top.
- Genetic Distance versus Physical Distance Ratios: A separate table of cM/Kbp for each map is provided at the bottom of the page. Click on the desired chromosome number in this table to view a graph of cM/Kbp versus Kbp for that chromosome.
The Combined Physical and Genetic Maps can be accessed by:
- Selecting "Physical and Genetic Map" from the Map type pull-down menu from Genomic View
- Selecting the "Physical and Genetic Maps" option from the Yeast Maps section of the Analysis & Tools contents page
- Clicking one of the sixteen chromosome numbers at the top of the
Sample Map to display the Combined Physical and Genetic Map for a desired
chromosome
- Entering the desired region in Gene/Sequence Resources and choosing "Combined Physical and Genetic Map" as the display method
Go to Combined Physical and Genetic Maps of S. cerevisiae
Return to Saccharomyces Genome Database