There is a great need for standards in the orthology field. Users must contend with different ortholog data representations from each provider, and the providers themselves must independently gather and parse the input sequence data. These burdensome and redundant procedures make data comparison and integration difficult. We have designed two XML-based formats, SeqXML and OrthoXML, to solve these problems. SeqXML is a lightweight format for sequence records-the input for orthology prediction. It stores the same sequence and metadata as typical FASTA format records, but overcomes common problems such as unstructured metadata in the header and erroneous sequence content. XML provides validation to prevent data integrity problems that are frequent in FASTA files. The range of applications for SeqXML is broad and not limited to ortholog prediction. We provide read/write functions for BioJava, BioPerl, and Biopython. OrthoXML was designed to represent ortholog assignments from any source in a consistent and structured way, yet cater to specific needs such as scoring schemes or meta-information. A unified format is particularly valuable for ortholog consumers that want to integrate data from numerous resources, e.g. for gene annotation projects. Reference proteomes for 61 organisms are already available in SeqXML, and 10 orthology databases have signed on to OrthoXML. Adoption by the entire field would substantially facilitate exchange and quality control of sequence and orthology information.

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.

BACKGROUND: Transmembrane (TM) proteins are proteins that span a biological membrane one or more times. As their 3-D structures are hard to determine, experiments focus on identifying their topology (i. e. which parts of the amino acid sequence are buried in the membrane and which are located on either side of the membrane), but only a few topologies are known. Consequently, various computational TM topology predictors have been developed, but their accuracies are far from perfect. The prediction quality can be improved by applying a consensus approach, which combines results of several predictors to yield a more reliable result. RESULTS: A novel TM consensus method, named MetaTM, is proposed in this work. MetaTM is based on support vector machine models and combines the results of six TM topology predictors and two signal peptide predictors. On a large data set comprising 1460 sequences of TM proteins with known topologies and 2362 globular protein sequences it correctly predicts 86.7% of all topologies. CONCLUSION: Combining several TM predictors in a consensus prediction framework improves overall accuracy compared to any of the individual methods. Our proposed SVM-based system also has higher accuracy than a previous consensus predictor. MetaTM is made available both as downloadable source code and as DAS server at http://MetaTM.sbc.su.se.