Embedding the NCBI Sequence View in Web Content

Introduction

The NCBI Graphical Sequence Viewer (SV) is a general purpose tool for viewing biological sequence data. The Sequence Viewer has a very rich set of options and can display virtually any sequence. It can be embedded in a wide variety of web pages serving many different needs. This page has examples showing best practice for embedding Sequence Viewer with several different sets of options.

The API Reference should be consulted for the full suite of options and parameters. Additional documentation can be found here: http://www.ncbi.nlm.nih.gov/projects/sviewer/help.html

Questions should be addressed to: sviewer-service AT ncbi.nlm.nih.gov

For users that want to embed the sequence viewer on their page, please pay attention to the cross-domain scripting section of the API Reference. Sequence Viewer makes use of AJAX and the EXTjs library and is tied to the infrastructure at NCBI; if you fail to adjust for cross-domain scripting, your embedding will not work.

For examples of sequence coordinate reporting using markers, see Marker Demo page. Another example is HGVS and SNP Search Demo.

View of single sequence with full frame decoration

View of single sequence with minimal frame decoration

Alignment View

Iframed Sequence View

Example below illustrates iframe embedding.
In this case, the Sequence Viewer instance is put into an iframe to avoid possible CSS and JavaScript interference with the main page. Sequence Viewer implements automatic iframe resizing to maintain vertical size budget and avoid unnecessary vertical scrolling. All user actions (zoom in and out, track reconfigurations, etc.) should automatically recalculate vertical size.