PubMed Nucleotide Protein Genome Structure Taxonomy

Avena sativa genome data and search tips Revised August 11, 2008

The Entrez Map Viewer help document describes the general features of Map Viewer. This page provides the descriptions of data and search tips specific to Avena sativa. You may return to the Avena sativa genome overview page to follow links to on-line help for Avena sativa bioinformatics.

  1. Scope of Data
  2. Display Customization
  3. Available Map
  4. Constructing Queries
  5. Constructing URLs

Scope of Data back to contents

Three points about genetic maps presented through MapViewer at NCBI 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 see Display Customization.

Frequency of Updates to Map Viewer Data back to contents

As data for other genetic maps becomes available, these maps will be presented.

Display Customization back to contents

To facilitate comparison between genetic maps, MapViewer can graphically indicate when adjacent maps have loci that are either the same classical genetic locus or recognized by the same molecular reagent, whether RFLP probe, RAPD primer, or AFLP primers. This capability is user-controlled via the Maps and Options link at the top of the MapView page. Enabling (mouse clicking) the "Show connections" option in the Maps and Options dialog box invokes the capability. The order of genetic map presentation (left to right across the window) is chosen in the Maps and Options dialog box. The Master Map, the right-most map, is chosen in either the Maps and Options dialog box or by clicking on the right-pointing arrow adjacent to the map identifier at the top of displayed maps. An unwanted map can be removed from the display by clicking on the "X" adjacent to the just-described arrow.

The "Verbose" mode, chosen in the Maps and Options dialog box, shows the ancillary information associated with the locus - name of the molecular probe (if any) and the GenBank accession(s) associated with the molecular probe. When there are multiple GenBank accessions corresponding to a particular molecular probe all are presented with the "|" character separating the individual accessions. When there is some particular significance to the order of multiple accessions, this will be provided in the map-specific subsection of Available Maps.


Available Maps back to contents

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

Avena atlantica x Avena hirtula, 1992 Map back to contents
The map was built from 44 F2 derived F3 families from the cross of Avena atlantica and Avena hirtula, two A-genome diploid species. This data was previously published: {O'Donoughue LE et al., Genome (1992) 35: 765-771} and Van Deynze, AE et al., (1995). Map units are cM.

Avena strignosa x Avena wiestii, 1994 Map back to contents
The map was built from 100 F8:9 lines. These were derived via single-seed descent from a F6:8 RI population by Dr. M. Lee {Iowa State University; Ames, IA} from the cross of Avena strignosa and Avena wiestii, two A-genome diploid species. This data was previously published: {Rayapati PJ et al., Theor Appl Genet (1994) 89:831-837}. Map units are cM.

Avena strignosa x Avena wiestii, 2000 Map back to contents
The map was built from 100 F8:9 lines. These were derived via single-seed descent from a F6:8 RI population by Dr. M. Lee {Iowa State University; Ames, IA} from the cross of Avena strignosa and Avena wiestii, two A-genome diploid species. This data was previously published: Yu, G-X and Wise, RP, (2000). Map units are cM.

Constructing queries back to contents

Searchable Terms back to contents

Text terms back to top

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:

  • symbols
  • alternate symbols
    A search for the GenBank accession BE438992 will retrieve the locus named Xbdc588-4A. Both terms refer to the same genetic entity. The terms are therefore considered synonyms and either term will retrieve the same information for viewing.
  • current names or text words that are part of names
    A search for ATpase will retrieve those map objects containing ATPase as part of their descriptions - i.e. XATPase-1D, XATPase-3A. XATPase-3B.1 and XATPase-3B.2.
    If multiple terms are entered, they will automatically be combined with a Boolean AND. For example, a query entered as "cell adhesion" will be processed as cell AND adhesion and will retrieve records with descriptions that contain cell matrix adhesion as well as cell adhesion. The section on Boolean Operators provides information about additional options. Searches of adjacent terms, adjacency searches, are not supported at present.
The specific terms available are:
    locus mnemonic, corresponding GenBank accession

The search program looks for the query term in the maps mentioned above. The search is case-insensitive - thus "XM*" and "xm*" 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 "cd*" will locate all of the loci with "cd" as the first two characters - i.e. cdo54 and cDbTUB30 as well as 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 Triticum aestivum, 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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