Search Your Baits

The Search Your Baits tool lets you retrieve and take action on your custom bait content. With this tool, you search for baits based on the annotation, accession, or sequence information that is associated with them. For a general discussion of baits, see Overview of working with baits.

You can set up a more generalized search in which you enter a single search term, and retrieve all baits that contain the term within any annotation or accession. For example, with a search type of All, if you type kinase as the search term, and do not require an exact match, the search returns all baits that have this word in their annotation, including baits with annotation such as protein kinase C, delta, and hexokinase 3. This is a good search methodology to use when you first explore the content of the database, and want to see what types of baits exist in the system. You can retrieve a single bait with a minimal amount of information, and you can also retrieve a large number of baits using more liberal search criteria. However, if your search criteria are too general, the method may retrieve many more baits than you want. To make this type of search more selective, you can require an exact match with the search term—For example, if your search term is Q005, baits with an accession or annotation value of Q0057 would not appear in your search results.

Another option with Search Your Baits is to set up a search that specifically searches one type of annotation or accession. The specific criteria include bait IDs, accession numbers, gene names, exact chromosomal coordinates, sequence, or cytobands. To return baits when it searches for a specific type of annotation or accession, eArray always requires exact matches, and when you set search parameters, you must specify values completely. You can also type or upload multiple search values, and eArray returns baits that match each of the values. This is a powerful search methodology that can retrieve a set of well-defined baits, or a single bait based upon a specific set of criteria. However, it can require a lot of effort to effectively define the parameters necessary to achieve the desired results, and it may be too stringent for your purposes.

Search Your Baits also lets you limit returned baits to those associated with a particular species, bait group, or library, and/or that are located within a specific folder.

Click the Workspace tab, or enter a collaboration.
Set the application type to SureSelect Target Enrichment or SureSelect RNA Enrichment.
Click Baits.

The Search page appears. Search Your Baits is selected by default.
In Search Type, select the desired option, then enter the desired search term(s) as described below for the specific type of search that you selected. For search types other than All, the program supports only exact searches.

Search Type	Instructions/Details
ALL	In this type of search, you specify a single search term. eArray retrieves baits that have any annotation or accession value that matches the search term. In Search Type, type the desired search term in the empty box. Do one of the following: To return baits that have an annotation or accession value that exactly matches the search term, including case, mark Exact Search. To return baits that have an annotation or accession value that contains the search term, without regard to case, clear Exact Search.
BaitID	Type a bait ID, or multiple bait IDs separated by pipe "\|" characters. The search returns baits whose IDs match exactly. A bait ID is a unique identifier for a bait. Alternatively, to upload a file that contains the desired bait ID data, click Upload, then select the desired file. The process is the same as the one described for probe searches in Upload data for probe searches.
Accessions	Type an accession, or multiple accessions separated by pipe "\|" characters. The search returns baits whose associated accessions are an exact match. An accession is a unique identifier that refers to a specific nucleotide sequence that is a target for the associated bait, or a protein sequence that is a product of the target. Specify accessions without sources. For example, list ref\|NM_015752 as NM_015752. Alternatively, to upload a file that contains the desired accession data, click Upload, then select the desired file. The process is the same as the one described for probe searches in Upload data for probe searches.
Cytoband	Type a cytoband identifier in the field. Separate multiple cytobands with pipe "\|" characters. The search only returns baits found in the listed cytobands. Follow this example format: 11p15.4 Alternatively, to upload a file that contains the desired cytoband data, click Upload, then select the appropriate file. The process is the same as the one described for probe searches in Upload data for probe searches and Genomic interval formats.
GeneSymbol	Type a gene symbol, or multiple gene symbols separated by pipe "\|" characters. The search returns baits with associated gene names that are an exact match. A gene symbol is a unique abbreviation that represents a gene, for example H3N1, or CTSB. Alternatively, to upload a file that contains the desired gene symbol data, click Upload, then select the appropriate file. The process is the same as the one described for probe searches in Upload data for probe searches.
ChromosomalLocation	Type a chromosomal location in the box, or multiple locations separated by pipe "\|" characters. The search returns any baits that map to the exact genomic coordinates that you specify. Alternatively, to upload a file that contains the desired chromosomal locations, click Upload, then select the appropriate file. See Upload data for probe searches. Note: This type of search retrieves baits based on matches with the exact genomic locations to which they map. To create baits that cover specific genomic regions or transcript sequences, use the Bait Tiling tool. See Bait Tiling (SureSelect Target Enrichment) and Bait Tiling (SureSelect RNA Enrichment).
BaitSequence	Type a valid bait sequence in the box, or multiple sequences separated by pipe "\|" characters. The search returns baits whose sequences are exact matches. To upload search sequences from a file, click Upload. See Upload data for probe searches.

Set the rest of the criteria for the search. These criteria further limit the list of returned baits.

Criterion	Instructions/Details
Folder	(Required) Select a folder from the list. The search retrieves baits only from the chosen folder. To include the folder's subfolders in your search, mark Include subfolders.
Species	(Required) Select the desired species.
Length	(Read-only) eArray supports a bait length of 120 nucleotides.
Used in Bait Groups	(Optional) If you set this criterion, the search returns baits only from the specified bait group(s). To specify bait groups, click Select and Add. The process is identical to the one described for selecting probe groups in Select probe groups for probe searches.
Used in Libraries	(Optional) If you set this criterion, the search returns baits only from the specified librar(ies).To specify libraries, click Select and Add. A library selection window appears. This selection window functions similarly to the one for probe groups described in Select probe groups for probe searches.
Bait Category	(Read-only, SureSelect RNA Enrichment application type only) eArray supports the RNA Capture baits, which retrieve specific RNA species from a pool of RNAs.

Click Search.

eArray begins the search. The search may take some time.

When eArray finishes the search, a Search Results pane appears, with the baits that match your search criteria. The bait search results are a gateway to many actions that you can take on baits. See What can be done with bait search results.

In addition, you can filter the bait search results:
- To apply your default filter to the list of baits, click Apply Default Filter.
  eArray removes the baits that do not satisfy the criteria of your default filter.
- To apply another filter to the list of baits, click Filter. In the list of filters that appears, in the Apply column, click Apply.
  eArray removes the baits that do not satisfy the criteria of the filter.

You create custom bait filters the same way that you create custom probe filters.

Note: If you do many similar searches on a consistent basis, you can customize eArray to pre-set certain search parameters. You can also customize the content and column order of search results. See Set user preferences.