Data Searches

To access the different data searches, click on the Search menu in the header and select the desired data type (Fig. 7).  To learn more about each search interface, please see the links below.

Figure 7.  Search menu in header.

 

Colleagues

The Colleagues Search allows for browsing a list of registered CottonGen users for the purposes of collaboration and assistance on Cottongen-related topics.

Figure 8.  CottonGen Colleague Search interface.

 

Genes and Transcripts

The Genes and Transcripts Search allows you to search sequences available in CottonGen using different parameters.  Some parameters return a broad range of results, while others can be used to find very specific data.  All genes/transcripts for a species can be selected (Fig. 9A) and either viewed together or filtered by name and/or location (Fig. 9B).  Searches can also be limited to datasets, such as genome and RefTrans assemblies or NCBI genes.

Figure 9.  CottonGen Genes and Transcript Search interface.

All search results are returned as a table with hyperlinks to more information (Fig. 10A).  The table can be downloaded, as well as a Fasta file of the returned sequences (Fig. 10B).  To do another search, click reset.

Figure 10. Gene and Transcript Search results table.

 

Genotypes

The Genotype Search can be accessed through the Search menu in the header.  By default, the search will be looking for SSR markers.  SNP markers can be selected by clicking the tab at the top of the User Interface (Fig. 11A).  Specific markers can be searched for by name, or the CottonGen marker database can be filtered by dataset (Fig. 11B), germplasm (Fig. 11C) and species.  SNP markers may also be filtered by chromosome or scaffold position (will be .  Note that setting multiple filters will only return results matching all criteria.

Figure 11.  CottonGen Genotype Search interface.

 

Results are returned in a table that can be downloaded in multiple configurations (Fig. 12A).  Hyperlinks can be used to view more detailed information (Fig. 12B).  Searches can be refined by editing the parameters or a new search can be initiated by clicking the reset button.

Figure 12.  CottonGen Genotype Search results.

 

Detailed marker information can be viewed (Fig. 13A), as well as associated alleles (Fig. 13B) and germplasms (Fig. 13C).

Figure 13.  CottonGen Genotype Search results details.

 

 

Germplasm

The Germplasm Search can be accessed through the Search menu in the header.  Information about germplasms linked to data in CottonGen can be searched by name, collection, pedigree, or country of origin (Fig. 14).  A list of germplasm names, in a text file, can also be uploaded to search for multiple germplasms at once.  

Figure 14.  CottonGen Germplasm Search interface.

Additionally, images associated with germplasm evaluation studies can be searched by germplasm name and keyword (Fig. 15).

Figure 15.  Searching images in CottonGen Germplasm Search.

Detailed information in the search results can be viewed by clicking the hyperlinks (Fig. 16).

Figure 16.  CottonGen Germplasm Search results.

 

Markers

To search the markers in CottonGen, click on the Search menu in the header and select Search Markers.  The Marker Search is useful for retrieving information about markers and can be broad or very specific depending on the parameters used.  Markers can be searched individually by name or in groups by uploading a text file with multiple marker names.  Filters can be set for marker type, cotton genome group, original marker species, and location (Fig. 17A).  Alternatively, searches may be performed on only those markers that are mapped or are near a specific locus or QTL.  Markers may also be browsed by associated genetic maps, chromosome positions, or genome groups (Fig. 17B).

Figure 17.  CottonGen Marker Search interface.

Search results are returned in table format, which is downloadable, as are associated sequences in Fasta format (Fig 18A).  Clicking on a marker name displays the marker's page with information such as alignments and map positions (Fig. 18B).  If you would like to change the search, either edit the parameters or click the reset button.

Figure 18.  Marker Search results.

 

Publications

To search publications on CottonGen, select Publication Search from the Search menu in the header.  This search functions the same as other literature searches but is limited to publications in the CottonGen database.  Publications can be searched using names or keywords in a number of fields (Fig. 19A).  The number of filters can be adjusted by clicking the Add/Remove buttons (Fig. 19B) and  a range of years can be specified (Fig. 19C). 

Figure 19.  CottonGen Publication Search interface.

The search results table has information about each publication (Fig. 20A).  By clicking the publication title, more detailed information is displayed.  Most publications also have a link to the publisher website or PubMed record in their titles (Fig. 20B).

Figure 20.  Publication search results and detailed publication information.

 

QTLs

Quantitative trait loci (QTLs) that are entered in CottonGen are searchable from the QTL Search option under the Search menu in the header.  QTLs may be searched using trait keywords, published symbols (see the Cotton Trait Ontology list in the Data header menu), or unique identifiers assigned by CottonGen.  

Figure 21.  CottonGen QTL Search interface.

The results are returned in a downloadable table (Fig. 22A) with hyperlinks to more information about the QTL, the map it is located on, and the associated trait name and symbol.  Clicking on the QTL label opens the overview page which has a link to map positions (Fig. 22B).  From the map position table, the QTL can be viewed in MapViewer or CMap. 

Figure 22.  CottonGen QTL Search results.

 

Sequences

To search sequences, select Sequence Search from the Search header menu.  This is useful for retrieving information about certain sequences from a larger dataset, or all the sequences from one or more datasets.  The Gene and Transcript Search is limited to genes and transcripts, whereas the Sequence Search includes other sequence types.  Use fewer filters to obtain broader results and more filters to narrow your results, as setting multiple filters will only return results matching all criteria.  This is not a BLAST search; that is available under the Tools menu. 

Sequence searches can be limited by species and sequence type (Fig. 23A).   The search can also be restricted to a certain genome dataset and further by chromosome or scaffold location (Fig. 23B).  The sequences in CottonGen can also be searched individually by name or in groups by uploading a text file with multiple names (Fig. 23C).      

Figure 23. CottonGen Sequence Search interface.

Search results are returned in a table with hyperlinks to more information (Fig. 24A).  The table can be downloaded, as well as a Fasta file of those sequences (Fig. 24B).  A new search may be performed by changing the filters or using the Reset button.

Figure 24.  CottonGen Sequence Search results.

 

Trait Evaluations

The Trait Evaluation Search can be accessed through the Search menu in the header.  This search retrieves phenotypic results from germplasm evaluation studies and is divided into Quantitative Traits (Fig. 25A) and Qualitative Traits (Fig. 25B).  Quantitative Traits are those that can be measured using numerical values.  Qualitative Traits are those that require the use of descriptors to evaluate.  

Figure 25.  CottonGen Trait Evaluation Search interface.

Quantitative Traits are searched by choosing the desired trait or traits from the pull-down menus (Fig. 26A).  This will autofill the value ranges based on the minimum and maximum trait values in CottonGen and can be restricted to narrow the search (Fig. 26B).  Results are displayed in a downloadable table (Fig. 26C) with links to further information on evaluated germplasms (Fig. 26D).

Figure 26.  Quantitative Trait Evaluation Search interface and results.

Qualitative Traits are searched by selecting the desired trait or traits from the pull-down menus (Fig. 27A), with the option to filter using available trait descriptors once the search page has auto-updated (Fig. 27B).  Results are displayed in a downloadable table (Fig. 27C) with links to further information on evaluated germplasms (Fig. 27D).

Figure 27.  Qualititative Trait Evaluation Search interface and results.