Integrating RNA web services in Jalview using JABAWS

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Abstract

Jalview is an alignment editor, originally developed for protein sequences, that is used in a variety of web pages and is also available as a stand-alone project. Jalview also includes a client that interacts with web services via JABAWS. In previous Google Summers of Code, students have worked to extend the functionality of Jalview to handle non-coding RNA sequences. Many web services already exist that are related to RNA, but they are not yet available to the Jalview client. During this Google Summer of Code, I will integrate the Annotate3D and RNAfold web services with Jalview using the JABAWS system.

Student

Tori Arendt

Mentors

Yann Ponty
Jim Procter

Important Links

Jalview and JABAWS Source
Jan Engelhardt's 2011 GSoC Project: PhyloSoC: Extending Jalview support for handling RNA
Lauren Liu's 2010 GSoC Project: PhyloSoC:Extending Jalview to Support RNA Alignment Annotation and Secondary Structure Visualization
Jalview
JABAWS
VARNA
RNAfold
Annotate3D

Timeline