Persephone can be started from the command line or via a web URL in order to search for a specific feature (or a set of features) such as a gene, a marker, a QTL, or a map (e.g., chromosome, genetic map, scaffold, organelle, and so forth).

Note

To call Persephone via a web URL you must use a web browser with .NET Framework support.

The command line parameters determine which feature to search for and which properties to consider while performing the search.

Searching Via Command Line

If you search for features through the command line, the parameters must be separated by spaces and query strings that contain spaces must be enclosed within double quotes. Asterisks (*) are interpreted as wild cards.

Example:

Persephone.exe annot_name=Sb04g* mapset_accession="Sorghum Annotation"

In the above example annot_name and mapset_accession are arguments passed to the Pesephone.exe application with values "Sb04g*" and "Sorghum Annotation".

Searching Via URLs

If the application is called via a URL, the parameters must be separated by ampersands (&) and query strings must be URL-encoded. For example, spaces must be converted to plus signs (+). Asterisks (*) are interpreted as wild cards.

Example:

http://your-server-name/Persephone.application?annot_name=Sb04g*&mapset_accession=Sorghum+Annotation

Using Optional Parameters

Optional parameters may be supplied in order to reduce the number of search results as well as to speed up the search. At most, one of these optional parameters should be supplied for every search request.

Optional Parameters for Searching Genes

The following table specifies the available parameters for searching gene annotations.

Note

Gene annotations can be searched by internal Persephone annotation ID, annotation name (mostly the name of a gene) and gene (annotation) qualifiers.

Gene Search Table:

 

Optional Parameters

Search By
(below)

organism_name

organism_id

mapset_accession

annot_name

annot_function

annot_id

annot_qualifier

 

  • annot_id: You can Search by Annotation ID alone to uniquely identify a single gene (particular splice variant in specific genome version), and immediately navigate to it.
  • organism_name/organism_id: Identifies a single organism, which may have different versions.
  • mapset_accession: Uniquely identifies a single organism/version combination.

Optional Parameters for Searching Markers

The following table specifies the available parameters for searching markers.

Note

Markers can be searched by marker keyword, marker name, and marker ID.

Marker Search Table:

 

Optional Parameters

Search By
(below)

organism_id

organism_name

mapset_accession

map_name

marker_keyword

marker_name

marker_id

mapping_id

 

  • mapping_id: Uniquely identifies a marker location on a single map.
  • marker_id: Uniquely identifies a marker, which may be aligned to zero or more maps.
  • marker_name: Identifies a marker, which may be aligned to zero or more maps.
  • marker_keyword: Specifies a keyword for marker search.
  • organism_name/organism_id: Identifies a single organism, which may have different versions.
  • mapset_accession: Uniquely identifies a single organism/version combination.
  • map_name: Restricts search to the given map.

Command Line Example:

Persephone.exe marker_name=umc2* mapset_accession="Corn Annotation"

In the above example, marker_name and mapset_accession are arguments passed to the Pesephone.exe application with values "umc2*" and "Corn Annotation".

URL Example:

http://your-webserver/Persephone.application?marker_name=Sb04g&mapset_accession=Corn+Annotation

Optional Parameters for Searching QTLs

The following table specifies the available parameters for searching QTLs.

Note

QTLs can be searched by QTL keyword, QTL name, and QTL ID.

QTL Search Table:

 

Optional Parameters

Search By
(below)

organism_id

organism_name

mapset_accession

map_name

qtl_name

qtl_keyword

qtl_id

 

  • qtl_id/qtl_name: Identifies a QTL, which may be aligned to zero or more maps.
  • qtl_keyword: Specifies a keyword for QTL search.
  • organism_name/organism_id: Identifies a single organism, which may have different versions.
  • mapset_accession: Uniquely identifies a single organism/version combination.
  • map_name: Restricts search to the given map.

Command Line Example:

Persephone.exe qtl_name=CQU* mapset_accession="Rice Annotation"

In the above example qtl_name and mapset_accession are arguments passed to the Pesephone.exe application with values "CQU*" and "Rice Annotation".

URL Example:

http://your-webserver/Persephone.application?marker_name=CQU*&mapset_accession=Rice+Annotation

Optional Parameters for Searching Maps

The following table specifies the available parameters for searching applications.

Note

Maps can be searched by map ID and map name.

Map Search Table:

 

Optional Parameters

Search By
(below)

from/to

mapset_accession

map_id

map_name

 

  • map_name: When specified together with mapset_accession it identifies a single map
  • map_id: Uniquely identifies a map.
  • from/to: When both "from" and "to" options are present it identifies a region on the map (in base-pair or centiMorgan units).
  • mapset_accession: Uniquely identifies a single organism/version combination.
  • mapset_name: Search for a map set by its name. Multiple results are possible.

Command Line Example:

Persephone.exe map_name=Chr.3 mapset_accession="Rice Annotation"

In the above example map_name and mapset_accession are arguments passed to the Pesephone.exe application with the values "Chr.3" and "Rice Annotation".

URL Example:

http://your-webserver/Persephone.application?map_name=Chr.3&mapset_accession=Rice+Annotation

Loading External Files from Command Line

Persephone can load external data files from disk or from external URLs. If you are calling Persephone via the command line use the “file” command line parameter followed by the file name or URL of the target file.

Examples:

Persephone.exe file=c:\data\rice.vcf
Persephone.exe file=http://your-server/rice.vcf
Persephone.exe file=ftp://user:password@your-server/rice.vcf

Please note query strings must be URL-encoded; in other words, spaces must be converted to plus signs (+). Asterisks (*) are interpreted as wild cards.

Supported File Formats

Supported file formats are identified by their file extensions, as follows:

Quantitative data:

  • BedGraph: ".bg", ".bedgraph"
  • Wiggle: ".wig", ".wiggle"

4-column or 5-column tabular format:

  • Comma-separated: ".csv"
  • Tab-separated: ".tsv"
  • Excel: ".xls", ".xlsx"

Variants:

  • Variant Call File: ".vcf"

Any of the files may be compressed in gzip or bzip2 format; for example, "methylation.bg.gz".

Search Parameter Examples

The examples below show implementation via web URL. The same functionality can be achieved via command line interface by methods described above.

Gene Annotations

  • Annotation ID: annot_id=200393504
  • Gene Name by mapset accession: annot_name=Sb04g0002*&mapset_accession=Sorghum+annotation
  • Gene Name by organism ID: annot_name=Sb04g0002*&organism_id=4558
  • Gene Name by organism name: annot_name=Sb04g0002*&organism_name=Sorghum+bicolor
  • Gene Function by mapset accession: annot_function=dwarf*&mapset_accession=Sorghum+annotation
  • Gene Function by organism ID: annot_function=dwarf*&organism_id=4558
  • Gene Function by organism name: annot_function=dwarf*&organism_name=Sorghum+bicolor
  • Qualifier by mapset accession: annot_qualifier=PTHR103*&mapset_accession=Sorghum+annotation
  • Qualifier by organism ID: annot_qualifier=PTHR103*&organism_id=4558
  • Qualifier by organism name: annot_qualifier=PTHR103*&organism_name=Sorghum+bicolor

Markers

  • Marker Keyword (including name): marker_keyword=dw2*
  • Marker on Map by MAPPING_ID: mapping_id=239758937
  • Marker on Map by map name and map set accession: marker_name=umc2331&mapset_accession=Corn+annotation&map_name=Chr.7
  • Marker on Map by map name and organism ID: marker_name=umc2331&organism_id=311987&map_name=Chr.7
  • Marker on Map by map name and organism name: marker_name=umc2331&organism_name=Zea+mays&map_name=Chr.7
  • Marker on Map by marker ID, map name, and map set accession: marker_id=84750253&mapset_accession=Corn+annotation&map_name=Chr.7
  • Marker on Map by marker ID, map name, and organism ID: marker_id=84750253&organism_id=311987&map_name=Chr.7
  • Marker on Map by marker ID, map name, and organism name: marker_id=84750253&organism_name=Zea+mays&map_name=Chr.7

QTLs

  • QTL Keyword (including name): qtl_keyword=cqu*
  • QTL on Map by MAPPING_ID: mapping_id=196496767
  • QTL on Map by QTL name, map name, and map set accession: qtl_name=CQU13&mapset_accession=Rice+annotation&map_name=Chr.3
  • QTL on Map by QTL name, map name, and organism ID: qtl_name=CQU13&organism_id=311988&map_name=Chr.3
  • QTL on Map by QTL name, map name and organism name: qtl_name=CQU13&organism_name=Oryza+sativa&map_name=Chr.3
  • QTL on Map by QTL ID, map name, and map set accession: qtl_id=196493260&mapset_accession=Rice+annotation&map_name=Chr.3
  • QTL on Map by QTL ID, map name, and organism ID: qtl_id=196493260&organism_id=311988&map_name=Chr.3
  • QTL on Map by QTL ID, map name, and organism name: qtl_id=196493260&organism_name=Oryza+sativa&map_name=Chr.3

Maps

  • Chromosome by MAP_ID: map_id=200313055
  • Chromosome by map name and map set accession: mapset_accession=Rice+annotation&map_name=Chr.3
  • Chromosome by map set name and map name: mapset_name=TAIR10&map_name=Chr.1
  • Chromosome region by MAP_ID: map_id=200313055&from=1000000&to=1500000
  • Chromosome region by map name and map set accession: mapset_accession=Rice+annotation&map_name=Chr.3&from=1000000&to=1500000

External Files

  • External file: file=c:\Sorghum.xls (may need to URL-encode the parameter)
  • External URL: file=http://www.your-server.com/variants.vcf (may need to URL-encode the parameter)