Searching Stock Lists on FlyBase

All stock lists contain stock numbers, genotypes, and stock center name. Some lists contain additional searchable information such as aberration breakpoints, transposon insertion sites, stock donors, and assorted comments (see the Stocks section of the FlyBase Reference Manual for information on individual stock lists). General search rules and genotype formatting conventions are provided below, followed by a set of examples that illustrate generally useful query strategies. Search strings are italicized in the examples.

Keep in mind that a query may not be the best way to find the information you need. The Bloomington and Szeged homepages contain an assortment of files organized for browsing.

General Search Rules

• An asterisk (*) serves as a wild card when placed at the beginning, middle or end of a character string. When using the search form, a wild-card is added to the end of your query string by default (uncheck the option box if you don't want a wild-card added).
• Alleles, aberrations, and transposons are represented in genotypes by their valid symbols. Stock lists cannot be searched with gene full names or with gene symbols alone; an allele must be specified or a wild card used in place of a specific allele symbol (gl[1] or gl* rather than glass or gl).
• Reserved characters include / , {, = and * . Even though these characters appear in genotypes, they cannot be used as literal characters in a search string.
• More than one search term can be included in a single search. The default operator when multiple search terms are specified is 'and' -- only records containing both terms are found. Use 'or' between terms in quick searches, or in the search form place your terms in separate boxes and toggle the operator box to 'or' to find all records with either or both terms. For example, cn* sp* will find all stocks that have both a cn and a sp allele. Use 'not' to find records that include the first and not the second term, for example cn* not bw* will find stocks that include a cn but not a bw allele. Expressions are evaluated left to right, e.g., cn* not bw* and w* is interpreted as (cn* not bw*) and w*.
• Superscripts are enclosed in square brackets ([]), and all allele symbols include superscripts (i.e., allele 1 is always explicitly written as a superscripted 1 rather than being implied by the absence of a superscript, and alleles of undetermined identity have an * as a superscript). Include the bracket when using a wild card to find all alleles to reduce irrelevant hits. For example, gl[* will find only gl and Gl alleles, while gl* will find, in addition, Gla and l(2)gl alleles and the balancer CyO-wglacZ.
• Cytological map positions appear in the Bloomington stock list with three digit division numbers and two digit band numbers (allowing these alphanumeric items to sort numerically in files provided for browsing). For example, 67C4-6 is recorded as 067C04-06, and 3C2 as 003C02. Searches must incorporate the leading zero(s) or a wild card. Cytological information is recorded in the Umeå and Szeged lists without leading zeros.

The full stock record will be displayed only when a single stock is found that meets your search criteria. Otherwise, a list of record titles including stock number, stock center, and genotype, which may be truncated, is returned if matches were found. Click on a stock number to see the complete record for that stock, or use the Batch options at the bottom of the page to retrieve multiple records at a time. The Refine query option at the bottom of the page allows you to do a secondary search on the search results if needed.

Examples

When using 'or' and 'not', keep in mind that the string you use to include or eliminate records can appear in any field of the record, not just the genotype field.

• To find a stock by its stock number, select the Stock Number field from the pull down menu and type in the stock number. When using the search form, uncheck the wild-card-addition option box to make a Stock Number search specific.
• To find all available alleles of a gene, ask for the gene symbol followed by [* , e.g., lt[* or l(2)01510[*. To find a specific allele, ask for the gene symbol followed by the superscript in brackets, e.g., lt[14].
• To find stocks with combinations of markers, list all gene-allele symbols in the same search, e.g., al[* pr[* sp[*.
• To eliminate a class of stock from the search results, use the 'not' operator. For example, to eliminate P transposon stocks from a search for ry alleles, use ry[* not P{*.
• To find a specific aberration stock, type in the full aberration symbol, e.g., Df(3R)by10 or Tp(1;Y)B3, or use a wild card in place of the aberration class and chromosomes involved, e.g., *)y[+]
• To find Bloomington stocks with aberration breakpoints or transposon insertion sites in a given division, ask for the three digit division number followed by *, e.g. 084*. Add the subdivision letter, e.g., 084B* to find all breakpoints within a given subdivision. To find all breakpoints in two or more subdivisions with one query simply list all of the desired subdivisions with 'or'. For example, the query 067B* or 067C* will return all stocks with a breakpoint in the interval 67B-C. Use the standard two digit format to find stocks from the Umeå and Szeged lists based on cytological information (e.g., 84B*).
• To find all P stocks with a specific construct, use the name of the construct symbol as your search term, e.g., lacW, PZ, lArB, neo, or CaSpeR.
• To find a P stock by laboratory acquisition name, use the lab short name bracketed by wild cards as the search term, e.g., *A103.1M2*, *B9-3-53*, *00053*, *neo6*.