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JPred4: a protein secondary structure prediction server.

Drozdetskiy A, Cole C, Procter J, Barton GJ - Nucleic Acids Res. (2015)

Bottom Line: Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results.Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions.Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.

View Article: PubMed Central - PubMed

Affiliation: Division of Computational Biology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.

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JPred4 results summary page (1) with the results of predictions presented in SVG (2). Links to detailed and simple reports in coloured HTML/PS/PDF formats (3). Example summary in HTML format is shown in (4) as well as the new addition of full multiple sequence alignments with and without gaps/insertions (5). On a separate linked page the user is able to run the Jalview applet (6) which allows a more sophisticated and interactive method of viewing the prediction results. Links to all the details for the prediction and an archive of the results are also available (7).
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Figure 2: JPred4 results summary page (1) with the results of predictions presented in SVG (2). Links to detailed and simple reports in coloured HTML/PS/PDF formats (3). Example summary in HTML format is shown in (4) as well as the new addition of full multiple sequence alignments with and without gaps/insertions (5). On a separate linked page the user is able to run the Jalview applet (6) which allows a more sophisticated and interactive method of viewing the prediction results. Links to all the details for the prediction and an archive of the results are also available (7).

Mentions: Figure 2 summarizes the main results page while Figure 3 shows examples of summary emails returned to a user for single or batch sequence submissions. Unlike previous versions of JPred, the primary visualization of a JPred4 prediction result is a scrollable SVG image. The SVG is generated by Jalview 2.9 (www.jalview.org) (36) run in command-line mode as part of the JPred4 web server processing pipeline so users do not need to run Jalview on their own computers. However, the JalviewLite Java applet result page is still provided for users working with Java-enabled browsers who prefer direct access to Jalview's sophisticated functions.


JPred4: a protein secondary structure prediction server.

Drozdetskiy A, Cole C, Procter J, Barton GJ - Nucleic Acids Res. (2015)

JPred4 results summary page (1) with the results of predictions presented in SVG (2). Links to detailed and simple reports in coloured HTML/PS/PDF formats (3). Example summary in HTML format is shown in (4) as well as the new addition of full multiple sequence alignments with and without gaps/insertions (5). On a separate linked page the user is able to run the Jalview applet (6) which allows a more sophisticated and interactive method of viewing the prediction results. Links to all the details for the prediction and an archive of the results are also available (7).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489285&req=5

Figure 2: JPred4 results summary page (1) with the results of predictions presented in SVG (2). Links to detailed and simple reports in coloured HTML/PS/PDF formats (3). Example summary in HTML format is shown in (4) as well as the new addition of full multiple sequence alignments with and without gaps/insertions (5). On a separate linked page the user is able to run the Jalview applet (6) which allows a more sophisticated and interactive method of viewing the prediction results. Links to all the details for the prediction and an archive of the results are also available (7).
Mentions: Figure 2 summarizes the main results page while Figure 3 shows examples of summary emails returned to a user for single or batch sequence submissions. Unlike previous versions of JPred, the primary visualization of a JPred4 prediction result is a scrollable SVG image. The SVG is generated by Jalview 2.9 (www.jalview.org) (36) run in command-line mode as part of the JPred4 web server processing pipeline so users do not need to run Jalview on their own computers. However, the JalviewLite Java applet result page is still provided for users working with Java-enabled browsers who prefer direct access to Jalview's sophisticated functions.

Bottom Line: Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results.Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions.Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.

View Article: PubMed Central - PubMed

Affiliation: Division of Computational Biology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.

Show MeSH