Sfixem--graphical sequence feature display in Java

DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System

SUMMARY

The rise in biological sequence data has led to a proliferation of separate, specialized databases. While there is great value in having many independent annotations, it is critical that there be a way to integrate them in one combined view. The Distributed Annotation System (DAS) was developed for that very purpose. There are currently no DAS clients that are open source, specialized for aggregating and comparing protein sequence annotation, and that can run as a self-contained application outside of a web browser. The speed, flexibility and extensibility that come with a stand-alone application motivated us to create DASher, an open-source Java DAS client. Given a UniProt sequence identifier, DASher automatically queries DAS-supporting servers worldwide for any information on that sequence and then displays the annotations in an interactive viewer for easy comparison. DASher is a fast, Java-based DAS client optimized for viewing protein sequence annotation and compliant with the latest DAS protocol specification 1.53E.

AVAILABILITY

DASher is available for direct use and download at http://dasher.sbc.su.se including examples and source code under the GPLv3 licence. Java version 6 or higher is required.

Accelerated discovery of novel protein function in cultured human cells

Experimental approaches that enable direct investigation of human protein function are necessary for comprehensive annotation of the human proteome. We introduce a cell-based platform for rapid and unbiased functional annotation of undercharacterized human proteins. Utilizing a library of antibody biomarkers, the full-length proteins are investigated by tracking phenotypic changes caused by overexpression in human cell lines. We combine reverse transfection and immunodetection by fluorescence microscopy to facilitate this procedure at high resolution. Demonstrating the advantage of this approach, new annotations are provided for two novel proteins: 1) a membrane-bound O-acyltransferase protein (C3F) that, when overexpressed, disrupts Golgi and endosome integrity due likely to an endoplasmic reticulum-Golgi transport block and 2) a tumor marker (BC-2) that prompts a redistribution of a transcriptional silencing protein (BMI1) and a mitogen-activated protein kinase mediator (Rac1) to distinct nuclear regions that undergo chromatin compaction. Our strategy is an immediate application for directly addressing those proteins whose molecular function remains unknown.

Improved and automated prediction of effective siRNA

Short interfering RNAs are used in functional genomics studies to knockdown a single gene in a reversible manner. The results of siRNA experiments are highly dependent on the choice of siRNA sequence. In order to evaluate siRNA design rules, we collected a database of 398 siRNAs of known efficacy from 92 genes. We used this database to evaluate previously proposed rules from smaller datasets, and to find a new set of rules that are optimal for the entire database. We also trained a regression tree with full cross-validation. It was however difficult to obtain the same precision as methods previously tested on small datasets from one or two genes. We show that those methods are overfitting as they work poorly on independent validation datasets from multiple genes. Our new design rules can predict siRNAs with efficacy >/= 50% in 91% of cases, and with efficacy >/=90% in 52% of cases, which is more than a twofold improvement over random selection. Software for designing siRNAs is available online via a web server at or as a standalone version for high-throughput applications.