Domains & Sites (PROSITE)

The Databases – Domains & sites (PROSITE) track searches chains against common patterns found in the PROSITE database (installed with your software). When you apply the method, Protean 3D will search the protein sequence against the pattern library and display found patterns and their labels. Protean 3D will attempt to locate the database automatically. If it is not found, you will be prompted to locate it.

By default, the PROSITE database (prosite.dat) is installed to the Prosite folder, found in the following directory:

• Windows 7 & Windows 8: C:\Users\Public\Documents\DNASTAR\Lasergene 10 Data\Prosite

• Macintosh: Hard Drive:Applications:DNASTAR:Lasergene 10 Data:Prosite

The following video is a brief walkthrough that shows how to use the Domains & Sites (PROSITE) track:

To apply this track to the sequence:

In the Tracks panel, expand Databases and check the box next to Domains & Sites (PROSITE). The track will now be visible in the Analysis view. In addition, a list of findings will appear in the Tracks panel under “Domains & Sites (PROSITE).”

To edit track options:

Select the track in the Tracks panel. Open the Track Options section, which appears as follows:

Choose whether you want to Skip Frequent Patterns or Show All Patterns. If you choose Skip Frequent Patterns (the default), Protean 3D will not display common sites, such as asparagine glycosylation and tyrosine kinase phosphorylation. Thus, fewer sites will be displayed.

Click if you wish to return to the default settings.

Working with PROSITE results:

In the Analysis view, the PROSITE synopsis shows all pattern hits found in a given cluster of chains. The patterns found in the same location in all chains are shown in solid color and in front of the sequence line. The patterns found only in some of the chains are shown as semitransparent and behind the sequence line.

Expanding the synopsis reveals separate rows containing patterns found in all chains and patterns found only in some of the chains. You can further expand the latter row to reveal two additional rows: "by pattern," and "by chain."

Task	How To
To view the residue range that falls within the pattern	Hover over any PROSITE pattern match shape in the Analysis View. By selecting a shape or marker, this information and additional information will be displayed in the Details panel.
To view the PROSITE entry online	Open the Details panel and click on the hyperlink in the “Actions” section. A browser window will open at the relevant PROSITE entry.
To search the PROSITE database online	Click the “Scan PROSITE” link at the top of the page.

*Note: DNASTAR is authorized by Geneva Bioinformatics (GeneBio) S.A. to incorporate PROSITE^® data into Lasergene. PROSITE^® is a registered trademark of the Swiss Institute of Bioinformatics (SIB) and GeneBio has been granted exclusive rights by the SIB for the licensing of PROSITE. Note that access to PROSITE via Lasergene requires a user license which can be obtained by contacting GeneBio at sib-db@genebio.com or info@genebio.com.