PubMed Nucleotide Protein Genome Structure Taxonomy

Lycopersicon esculentum genome data and search tips Revised June 2, 2003

The Map Viewer help document describes how to use the Map Viewer software. This page describes the data available for Lycopersicon esculentum (tomato), and the search tips specific to that organism. You may return to the Lycopersicon esculentum genome overview page to follow links to on-line help for Lycopersicon esculentum bioinformatics. The Map Viewer home page allows you to search the genome data of any organism represented in MapViewer.

  1. Scope of Data
  2. Available Maps
  3. Constructing Queries
  4. Constructing URLs

Scope of Data back to contents

Three points about genetic maps need to be emphasized. First, genetic maps usually are generated as a close-ended project. When the map is offered to the public there is little refinement afterwards. Second, the unit of a genetic map is the cM, computed from the frequency of recombination between two segregating loci. Thus the determined size of a chromosome, in cM, depends upon the extent of the chromosome between the most separated markers and may vary between different genetic maps. Third, correlation between genetic maps is only possible to the extent of comparison between the loci common to the maps under comparison. To facilitate comparison between genetic maps, MapViewer can graphically indicate a locus that is common to adjacent maps. This capability is user-controlled via the "Display settings" link at the top of the MapView page. Checking (mouse clicking) the "Show connections" option in the "Display settings" dialog box invokes the capability. The order of genetic map presentation (left to right across the window) is also chosen in the "Display settings" dialog box.

The "Verbose" mode, chosen in the "Display settings" dialog box, shows the GenBank accession(s) associated with the molecular probe.


Frequency of Updates to Map Viewer Data back to contents

The maps are all completed endeavors.

Available Maps back to contents

Currently four maps are available. As other map data is acquired, these maps will be noted as being available.

Genetic map, 1992 back to contents
This map was built using an F2 population from a backcross to L. pennelli of the interspecific cross of L. esculentum (LA1500) X L. pennellii (LA716). The data was previously published in Bernhatzky R and Tanksley SD; Genetics 1986; 112:887-898. Map units are cM.

L. esculentum X L. pennellii; 1986 back to contents
This is the first plant genetic map where most of the loci are detected by DNA molecular markers. The map was built using an F2 population from a backcross to L. pennelli of the interspecific cross of L. esculentum (LA1500) X L. pennellii (LA716). The work was published previously in Bernhatzky R and Tanksley SD; Genetics 1986; 112:887-898. Map units are cM.

L. esculentum X L. pennellii; 1992 back to contents
This map was built using an F2 population derived from the interspecific cross of L. esculentum cv VF36-Tm2a X L. pennelli LA716. The details of the work are available in Tanksley SD et al (1992). Map units are cM.

L. esculentum X L. pennellii; 2000 back to contents
This is the tomato genetic map of conserved ortholog set (COS) markers for dicotyledon plants. The details of the work are available in Fulton TM et al (2000). Map units are cM.

Constructing queries back to contents

Searchable Terms back to contents

Text terms back to contents

The current version implements searching of flat files. The viewer supports searching on any text term that may describe an element on the map. These include:

  • locus mnemonics
  • alternate mnemonics
  • current names or text words that are part of names
    A search for '*d1*' will retrieve those map objects containing 'd1' anywhere as part of their descriptions. Likewise a search for 'ct163*' will find the different loci recognized by the probe "CT163".
The specific terms available for each map are:
  • Genetic; 1992
      • locus mnemonic, alternate name, corresponding GenBank accession
  • 1986 molecular map
      • locus mnemonic, alternate name, corresponding GenBank accession
  • 1992 molecular map
      • locus mnemonic, alternate name, corresponding GenBank accession
  • 2000 molecular map
      • locus mnemonic, alternate name, corresponding GenBank accession

The search program looks for the query term in the maps mentioned above. The search is case-insensitive - thus "CDO*" and "cdo*" will identify the same genetic sites.

Truncation back to contents

Search terms can also be truncated using an asterisk (*) as a wild card to represent zero to many characters. For example "rz*" will locate all of the loci with "rz" as the first two characters - i.e. rz672a, rz251a and others. To locate sites using a search string that is embedded in the target, for example "uaz*" and "rz*" using 'z', the search string needs an asterick (*) as the leading character - i.e. *z* will locate both "uza*" and "rz*". Searches of adjacent terms, adjacency searches, are not supported at present. See the truncation section of the general Map Viewer Help document for more details.

Map Positions back to contents

As noted in the Search By Position section of the Entrez Map Viewer general help document, there are three main ways to search by map position from the Map View of a chromosome:
  1. enter a range of interest in the Region text boxes in side bar
  2. click on the region of interest in the chromosome thumbnail graphic in the sidebar
  3. click on a region of interest in the enlarged Map View of the chromosome

For Zea mays, the following types of map positions can be entered in the Region text boxes noted in option 1:
  • symbols - you can enter gene symbols, marker names, or alternate symbols or marker names to display a region of the chromosome between those mapped elements. Note that both elements must be present on the map in order for the range search to work properly.

Query options back to contents

Boolean Operators back to contents

Boolean operators in a query are not currently supported.

Advanced Search Page back to contents

The Advanced Search page is currently under development.

Constructing URLs that link to Map Viewer back to contents

If you would like to create WWW links to the Map Viewer, the instructions for constructing URLs are given in the general Map Viewer Help document. You can construct URLs that either perform a search or display a specific mapped object or chromosomal region.

Questions or comments:
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