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This help document answers the following questions about the Molecular Probes and Clones Query Form:

• What can I use the Molecular Probes and Clones Query Form to find?
• How do I use this query form?
• What values are acceptable in each of the fields?
• How do I interpret the summary results of my query?
• Can I view a more detailed result? How do I interpret a detail report?
• Are there examples of queries and results?

See also:

• MGI Glossary for unfamiliar terms (or for how MGI defines specific terms) and acronyms.
• General Guidelines for Searching MGI
• Help Using Wildcards

What can I use the Molecular Probes and Clones Query Form to find?

The MGI database contains information on probes, clones, primers, BACs, YACs and STSs. Information may include the origin of the probe/clone, sequence, vector type, hybridizing loci, RFLPs, and references. Use the Molecular Probes and Clones query form to search for information on probes/clones associated with markers.

MGI also provides options to search for information on genetic polymorphisms extracted from probe/clone records in the database. Use the RFLP/PCR Polymorphism Query Form to search for such information directly. See Using the RFLP/PCR Polymorphism Query Form for how to do this.

How do I use this query form?

To search for detailed data using this query form, enter or select values in one or more of the query form fields described in the following paragraphs. After entering values in the form fields, click Search to submit the query. Click Reset to clear the fields and return any default values. See Using MGI Query Forms for answers to questions such as:

• How do I submit a query?
• What are operators and how do they affect my query?
• How do I select more than one item on a list?
• Does it matter what case I use when I type values in the fields?
• How do the sort options work?
• Is there a maximum number of results I can get back all at once?
• Is there a way to speed up a query?
• When I enter exact marker or gene symbols in the Marker Range boxes, do the query results include or exclude those markers?

What values are acceptable in each of the fields?

Gene/Marker Symbol/Name | Type | Map position | Probe/Clone Name | Sequence Type | Vector Type | Species | Strain | Tissue | Library | Clone Collection | Probe Accession ID | Sort by | Maximum returned

Gene/Marker	Gene/Marker Symbol/Name Symbol, name, or synonym for a mouse genetic marker. Enter one or more symbols/names/synonyms (separated by commas). Note: If the term itself contains a comma, put the entire term in quotation marks to ensure that the search is on the exact phrase (example: "cyclin B1, related sequence"). By default, the search is on current symbols/names and synonyms. However, you can limit the search to current symbols (no search of gene names) or to current symbols/names only (no synonyms). The operators (begins, = , ends, contains, like) present additional search options. The default is contains. To exclude symbols from a search, click NOT, select an operator, enter the symbol, and set the search criteria. Note: Many genes have withdrawn symbols and synonyms. If you click NOT and use the default setting, a gene appears if any of its symbols (including withdrawns and synonyms) do not match the query. Therefore, in apparent contradiction of your intent, some genes appear whose current symbol matches the query. You may find it more useful to change the selector to current symbols when using the NOT operator. Use the Sort by option, located at the bottom of the query form to retrieve results in Marker Symbol order. Type Use this field search for markers of selected marker type(s). Options are: gene, DNA segment, cytogenetic marker, QTL, pseudogene, BAC/YAC end, other genome feature, complex/cluster/region, microRNA, and All of the above (the default).
Map position	Use the map position parameters (Chromosome(s), Genome Coordinates, Cytogenetic Band, Marker Range, and cM Position) to limit the scope of your query. When using chromosome(s), you can also define genome coordinates, cytogenetic band, or cM position. You cannot combine genome coordinates, cytogenetic band, and cM position with one another. You can enter any markers with coordinates. See Using Map Position Fields on MGI Query Forms for further details about entering values in these fields.
Probe/Clone attributes	Probe/Clone Name Name of the probe/clone assigned by the author of the article where it is reported or by MGI curators. The probe/clone name does not necessarily identify a probe/clone uniquely. Use the Sort by option (located at the bottom of the query form) to retrieve results in Probe Name order. Sequence Type Select one item from the drop-down list (the default is All). You can focus your search on probes/clones of a selected sequence type. Choices are: All, cDNA, genomic, DNA (construct), mitochondrial, oligo, primer, RNA, or Not specified. Use the Sort by option (located at the bottom of the query form) to retrieve results in Sequence Type order. Vector Type Select one item from the drop-down list. You can focus your search on probes/clones of a selected vector type (BAC, cosmid, P1, PAC, phage, phagemid, plasmid or YAC). The default is to return any information in the MGI database for each list item.
Probe/Clone source	Species Origin of the source. You can limit your search to probes/clones from one or more selected species. Strain Type in a (mouse) strain of origin. The default is CONTAINS, but using the = (equals) operator is fastest if you know the exact strain name. You can use BEGINS , but the search may be slow. MGI is not case sensitive, so you can use either capital or lowercase letters; for example, c57bl/6j or C57BL/6j. See MGI Strains for a list. Tissue Type in the tissue of origin. You can search for probes/clones derived from a specified tissue. See Molecular Segments - All Mouse Tissues for a list. Library Type in the strain library origin. You can type in the whole, or part of, the name of a library to search for clones belonging to that library. See MGI Clone Libraries for a list.
Clone Collection	Clone Collection To restrict your search to probes with a clone ID, select one or more of the clone collections from the selection list. Use the default (ANY) if you do not want to restrict the search by clone collection. For more information, see Using the Clone Collection Field on MGI Query Forms.
Accession ID	Probe Accession ID An MGI probe/clone record may be associated with several accession IDs including the MGI Accession ID (the unique ID assigned a probe/clone record in MGI), and other accession IDs such those from GenBank, IMAGE, WashU, and UniSTS. You can search by any accession ID assigned to a probe/clone. See Using the Accession IDs Query Form for more details.
Sorting and output format	Sort by Click one of the following choices depending on how you want any results ordered: Probe Name, Sequence Type, Marker Symbol, or Chromosomal Location. Maximum returned If you want to limit the number of results, type in a number. The default is 500. You can change this number to whatever you wish or you can click No limit. The intent of the default is not to speed the search by limiting the scope but rather to let you restrict (or expand) your results.

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How do I interpret the summary results of my query?

See Using the Molecular Probes and Clones Summary Report.

Are there examples of queries and results?

The following examples show the field values to type in for the search. Otherwise, default values on the form are assumed.

1. Find any DNA sequence accession numbers associated to a particular molecular segment record.

   Probe Accession ID:  MGI:12399
   

   A Molecular Probes and Clones Summary report appears. Click the clone ID link to access the Molecular Probes and Clones Detail report. The References section lists any available DNA Sequence Accession IDs with links to public sequence databases (e.g., GenBank, EMBL, DDBJ) and to the MGI Sequence Detail page. The report also lists any polymorphism data.

2. Find all the cDNA clones for the Chrng gene.
   

   Marker Symbol/Name: begins Chrng
   Sequence Type: cDNA
   

   The result is a list of all Chrng cDNA clones in the MGI database.

3. Find any cDNA clones mapped to Chromosome 1 between 40 and 50 cM, inclusive.

   Chromosome(s) 1
   cM Position between 40 and 50
   Sequence Type cDNA
   Sort by: Chromosomal Location
   

   The result is a list of cDNA clones associated with genes located on Chr 1 between 40 and 50 cM, ordered by chromosomal location.

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