PICTURE VIEW of Sequence-2

 

 

 

 

Mousing over the methods, provides a pop-up box, which gives the boundaries of the method, its match status, its E-value and the name of the method. The latter is not necessarily the Short_Name of the InterPro entry.

 

 

TABLE VIEW of Sequence-2

 

A Table View is provided for each InterPro entry featured in the Picture View. The Table View provides hyperlinks to member databases for the method or methods , which defines the entry. The name of the method, its E-value to Sequence-2 and the status of the match are given. In this example, it can be seen that the E-value for each PRINTS position specific scoring matrix (PSSM) is provided along with the match status.

 

It is worth checking the PRINTS website, to ascertain the number of PSSM’s associated with the PRINTS method. Any reduction in the number of PSSM’s is an indicator of an overall  FALSE POSITIVE match of the method to the protein sequence. 

 

 

 

The InterPro entry accession and those of its PARENT/CHILDREN are hyperlinked to the InterPro view of the entry.  GO terms are linked to the relevant information and the lineage of the term in the GO database.

 

 

 

RAW OUTPUT Sequence-2

Provides a tab delimited text file of the match information for each method, which includes the provided sequence name and its CRC64 if it already exists in the database.

 

 

XML OUTPUT of Sequence-2

Provides the XML output for the information provided in the Picture View.

 

 

Relationships between the returned entries:  IPR000276, IPR000610 and IPR002231.

 

It can be seen from the returned Picture View of Sequence-2 that all three entries are classified as FAMILIES. By studying the information provided in the Table View the relationships between these families can be seen.

 

 

To go to the InterPro view of the InterPro entry click on the hyperlinked entry accession number or on

 

the InterPro box:  

 

To go to the SRS view of the of the InterPro entry click on the SRS box:   

 

 

In the InterPro View the family tree can be displayed by clicking on [tree] in the left hand column:

 

 

           

 

 

 

 

 

Clicking on  expands that lineage:

 

 

 

Clicking on the entry accession takes you to the entry page for that accession.

 

 

 

 

 

In the SRS view of the InterPro entry, no tree display is provided. The tree is navigated by clicking on either the red or blue triangles.

 

 

 

 

The relationship between the returned entries  IPR000276,  IPR000610 and IPR002231

 

IPR000276 is the PARENT of  IPR00223, which in turn is the PARENT of  IPR000610.

 

IPR000610 is therefore the most specific match and Sequence-2 codes for a 5-Hydroxytryptamine 1A receptor.

 

 

 

 

  1. From the InterProScan results in SRS, link to the appropriate GO terms by choosing 'Link', then ticking GO and 'Submit link'. This is another way of retrieving the associated GO terms and all other InterPro entries these terms are associated with by using the GO links.

This retrieves: