Search tips

* If you have problems searching that can't be solved with the information on this page, please contact us. It may be that there are errors in the underlying database . . .

  1. Advanced Symbol Search: The "does not contain" option in the gene dropdown only works in the last position (ie., it only works in the third "gene" slot)
  2. Simple search: The Simple Search is not currently searching gene symbols and is therefore not returning stocks (for instance, deficiency stocks) where the gene name does not appear in the symbol or the comment.
  3. Advanced Symbol Search: The chromosome field appears to be attached to the remaining fields with an incorrect Boolean "OR" instead of the correct "AND".

Simple Stock Search

Use the Simple Stock Search to search for living BDSC stocks using one or more of the following stock attributes:
- stock number (if there is an exact match to a stock number, the search will show this result and no others)
- gene symbol (not gene name - see below for more information on using gene symbols)
- genetic symbol
- text from a genotype
- text from a comment
- donor name

Note that wildcards are automatically added to both ends of a text-based search term and that multiple search terms are automatically connected with a Boolean "AND".

Searches using multiple terms may be slow

When searching using gene symbols that are only one or two letters long, we strongly recommend using the Advanced Symbol search and using the "exactly matches" option to exactly match the gene symbol. 

Advanced Stock Search

Use the Advanced Stock Search to search for living BDSC stocks using any or all of the following stock attributes:
- text in a genotype
- text in a stock comment (see below for notes on stock versus symbol comments)
- donor name or organization (see below for notes searching donor information)
- affected chromosomes

General instructions
1. Enter a search term into one or more of the genotype, stock comment or donor boxes (one term per box). NOTE: If using an insertion symbol directly from FlyBase, use either the Simple Search or the Advanced Symbol search (insertion symbols from FlyBase do not contain markers whereas insertions in genotypes usually contain markers and therefore will not perfectly match).

2. To specify affected chromosomes, select from the affected chromosomes dropdown.

The affected chromosomes are simply the chromosomes in a stock known to carry an allele, insertion or aberration. Referred to as "Chr_all" in old style BDSC stock reports.

examples:
GenotypeAffected chromosomes
w[1118]1
sna[Sco]/CyO, P{sevRas1.V12}FK12
w[1118]; sna[Sco]/CyO, P{sevRas1.V12}FK11;2
w[*]; Kr[If-1]/CyO; D[1]/TM3, Ser[1]1;2;3

3. To add a Boolean 'AND' between genotype search terms, select 'Match all genotypes'. To add a Boolean 'OR' between genotype search terms, select 'Match any'.  (A Boolean 'AND' is automatically used between the remaining types of search terms.)

4. To add wildcards, select from the dropdown next to the search data type.

wildcard dropdown termdescription
containsadds wildcards to both ends of the search term
starts withadds a wildcard to the end of the search term
ends withadds a wildcard to the beginning of the search term
exactly matchesno wildcards

5.  Click "Find stocks"

6.  In the search results, click anywhere in an individual result to see a detailed report with any available stock comments, associated symbols with genes, symbol comments and map data, donors and associated IDs.

7. To order a stock, click "Add to cart" and complete the checkout process.

Advanced Symbol Search

Use the Advanced Symbol Search to search for allele, insertion and aberration symbols carried in living BDSC stocks using any or all of the following symbol attributes:
- text in a symbol name (remove any markers from an insertion symbol before using in this particular search)
- gene symbols (not gene names, see below for more information on using gene symbols)
- symbol comments (see below for information on stock versus symbol comments)
- for insertions only, you can specify the chromosome
In the search results, you can select one or more symbols and find stocks carrying those symbols.

General instructions
1. Enter search terms into one or more of the gene, symbol, or symbol comment boxes (one term per box). NOTE - for genes, you must use a valid FlyBase gene symbol (not gene name) or, in some cases, a tool symbol. See below for more tips on doing gene/tool searches. Be sure to remove any markers from an insertion symbol before using.

2. To add a Boolean 'AND' between gene search terms, select 'Match all'. To add a Boolean 'OR' between gene search terms, select 'Match any'.  A Boolean 'AND' is automatically used between the remaining types of search terms.

3. To add wildcards, select from the dropdown next to the search data type.

wildcard dropdown termdescription
containsadds wildcards to both ends of the search term
starts withadds a wildcard to the end of the search term
ends withadds a wildcard to the beginning of the search term
exactly matchesno wildcards

4. Click 'Find Symbols'

5. In the search results, click anywhere in an individual result to see a detailed report with associated genes, comments and any mapping data associated with the symbol.

6. To find stocks, select the desired symbol(s) by checking the box on the left side and then click 'Find Stocks'. See steps 6 and 7 above to see stock details and add stocks to your cart.

More help:

We use FlyBase gene symbols as well as some FlyBase tool symbols in our database. See below for tips on using each.

Gene symbols:

Our database uses the FlyBase gene symbol, not the gene name (ie., we use "Dl" and "per", not "Delta" and "period"). In addition, non-D. melanogaster genes include the 4-letter species prefix used by FlyBase (D. melanogaster genes are not prefixed by "Dmel" in our database). We do not currently have the capacity to handle full gene names or gene synonyms.

When searching using gene symbols that are only one or two letters long, we strongly recommend using the Advanced Symbol search and using the "exactly matches" option to exactly match the gene symbol.

When searching genes using “exactly matches” on the Advanced Symbol search, the gene symbol must exactly match the official FlyBase symbol and Greek symbols must be spelled out. For example:
1. use "N" not "Notch" or "CG3936"
2. use “DCTN1-p150” not “p150” or “dynactin”  or “CG9206”
3. use  CG10326 (this gene has no official non-CG name)
4. use "alphaTub84B" not "αTub84B" or "α-Tubulin at 84B"
6. use “Hsap\ATXN1” not “ATXN1” or  “Ataxin1”

Similarly to using “exactly matches”, when searching genes using “contains”, “ends with” or “starts with”, the text used must match the corresponding text of the official FlyBase gene symbol. For example:
1. a search using gene “starts with” “scar” will find symbols associated with SCAR and a bunch of scaRNAs but will not find scarlet alleles or transgenes because the symbol for scarlet is “st”
2. a search using gene “contains” “delta” will find symbols associated with ATPsyndelta, deltaCOP, E(spl)mdelta-HLH and 10 other genes with “delta” in the name but will not find Delta alleles or transgenes because the symbol for Delta is “Dl”.

We note that using "contains" or "ends with" is a good way to avoid having to use the species prefix when hunting using non-D.melanogaster genes. For instance, to search for insertions carrying human APP, search using gene "contains" "APP".

Tool symbols:

In some cases, we are now using tool symbols in place of gene symbols. Generally, we do this for one of two reasons:

1. FlyBase has obsoleted the gene in favor of a tool.  For instance, FlyBase obsoleted many foreign genes that represented regulatory sequences (e.g. Scer\UAS, Scer\FRT) and replaced them with tools (e.g., UAS, UASt, UASp, FRT).

2. It makes more sense to link to a tool than to the gene.  For instance, in stock reports for split GAL4 lines, you will now see links to the split GAL4 DNA-binding domain tool report (GAL4(DBD)::Zip-), which has a nice explanation of the split GAL4 system, rather than to the Scer\GAL4 gene report. Similiarly, stock reports for stocks carrying sensors, optogenetic tools etc., now often link to the FlyBase report for the tool (e.g. Voltron, csChrimson, GCaMP6f) rather than to the gene(s) used to make the tool.

When searching using tool symbols using “exactly matches” on the Advanced Symbol search, the tool symbol must exactly match the official FlyBase. As with using gene symbols, often the best approach is to use "contains" to put a wildcard on either end of your search term thus maximizing the chances of returning the stocks you are looking for.

You can refine your search by selecting qualifers in the dropdown to the right of the search box.

Dropdown termDescription
all categoriessearch all categories
allelesearch for non-insertion-based gene alleles (alleles made by EMS, X-ray, P excision, homologous recombination etc); this term also pulls in FRT-based single gene alterations
codingsearch for insertions carrying coding sequence for the gene
coding and regulatorysearch for insertions carrying both coding and regulatory sequences for the gene
deficiency or putative deficiencysearch for deficiencies that delete or may delete the gene
gene trapsearch for insertions carrying sequences that are or may be influenced by neighboring genomic sequence (e.g., GAL4 or lacZ enhancer traps)
guideRNAsearch for guide RNAs for the gene
inserted or swapped insearch for insertions in the gene (includes both transposon- and homologous recombination-based insertions)
noncoding RNAsearch for insertions carrying a noncoding RNA gene
potential misexpressionsearch for insertions carrying UAS sequences that might be used to direct expression of nearby genes (e.g., P{EP}, P{EPgy2}, P{XP} etc)
protein binding site (eg., FRT or loxP site)search for non-regulatory defined DNA sequences (e.g., recombinase target sites etc)
protein trapsearch for insertions in coding introns carrying sequences that are or may be spliced into mRNAs and incorporated into proteins (e.g., FlyTraps)
regulatory or putative regulatorysearch for insertions carrying regulatory or putative regulatory sequences from the gene
RNA spongesearch for insertions carrying RNA for sequestering the gene transcript
RNAisearch for insertions carrying sequences for RNAi of the gene
wildtype allelesearch for wild-type alleles of the gene
Zn finger nucleasesearch for insertions carrying a Zn finger nuclease that targets the gene

Our database does not support the use of Greek symbols. Greek symbols must be spelled out. For example:
- use "betaTub85D", not "βTub85D"
- use "Delta2-3", not "Δ2-3"

Searches are not case sensitive, for instance, "Dl" and "dl" will yield the same result

Non-D. melanogaster gene symbols in our database contain the 4-letter species prefix used by FlyBase. We suggest using gene “contains” for searching non-D. melanogaster genes to avoid having to add the species prefix.

examples:
1. use "contains" "GFP" instead of "exactly matches" "Avic\GFP"
2. use "contains" "APP" instead of "exactly matches" "Hsap\APP"

Beware that many fluors are derivatives of other fluors, for example, BFP and YFP are really variants of GFP.  FlyBase lists all insertions carrying fluor derivatives under the parental gene and we do as well.  To find GFP and RFP derivatives like BFP, mCherry or Tomato, we suggest searching the symbol name or browsing our fluor pages.

We are not currently curating non-fluorescent tags (e.g. His, Myc, FLAG etc), so you cannot use our database to search, for example, all transgenes tagged with His for a particular gene.

In some cases, this information is captured in the symbol name or is in a comment, so you can try using the Advanced Symbol search to search for a particular gene plus a text string (like His or Myc) in the symbol name or comment. If you don't get any results from your search, it doesn't necessarily mean that what you are looking for doesn't exist, only that the non-fluorescent tag isn't in the symbol or comment. We recommend using our links to FlyBase to identify the exact components present in a symbol of interest. This may also require delving into the primary publication.

First - let us say that, in most instances, you are probably going to want to search symbol comments (in the Advanced Symbol Search) versus stock comments (in the Advanced Stock Search).  Here's why . . .

Stock comments are comments that are relevant only to the stock as a whole. The vast majority of these comments contain information on segregating ("floating") alleles or balancers or the expressivity of common markers (like Cy[1] or sna[Sco]). Some stock comments do carry other kinds of information about a stock (e.g., the background, Wolbachia status or the function/use of the stock as a whole) but most descriptive information is found in symbol comments.

Symbol comments carry information about individual transgenes, alleles and aberrations found in stocks. Most often these comments are descriptions of transgenes, but they can also include information on mapping data not found in the "Map" section of a symbol or stock report, information on mutations, lethal/viable/sterile data etc. Because some symbols are present in multiple stocks, these comments, by necessity, must pertain to the symbol in isolation and not, for instance, how it might be used in the context of one particular stock. 

Be aware that we generate symbol comments at the time of donation so some information may be incomplete or out of date. On most of our pages, clicking on the symbol will take you to its respective FlyBase report where you can find the latest data curated by FlyBase.

You may search using either the donor's name or organization. 

Be aware that the organization listed is the one associated with the donor at the time of the donation and may not be where the donor is currently. 

Because first (given) names can vary dependent on the context (Sue versus Susan, Dave vs David), we recommend using "contains" and only the last or family name when possible.

Searching for something you know is there but not getting any results? See below for some troubleshooting tips.  If nothing below applies to your situation, please contact us.

SituationSolution
Searching using a general search termOur system may time out if there are too many search results. Try refining your search terms.
Advanced stock search
Searching genotypes using an insertion symbol from FlyBaseBDSC genotypes include the construct marker (ie., 'w[+mC]=, 'y[+t7.7]='' etc) in the insertion name. We include the marker because most of the time you want to know what markers you are looking for when you are using a stock. FlyBase leaves the marker out because it is easier to read and you don't care so much about the marker when you want to know who has used it and what it does. When searching using an insertion symbol from FlyBase, we recommend using the Advanced symbol search (our genotype database shows markers but our symbol database does not . . .).
Advanced symbol search
Searching for an allele on a specific chromosome.You cannot specify a chromosome when searching for an allele. Please remove the chromosome criteria.
Searching symbols using an insertion symbol from a BDSC genotypeInsertions in our 'symbols' database do not include markers. Please remove any markers (ie., 'w[+mC]=', 'y[+t7.7]='' etc) from the symbol or use the Advanced genotype search.
Searching for two components on the same chromosome.Our database does not hold information about which components are on the same chromosome in any one particular genotype so this is not a do-able search . . .