W444–W450 Nucleic Acids Research, 2007, Vol. 35, Web Server issue doi:10.1093/nar/gkm364 ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ C. del Val1,2,*, P. Ernst1, M. Falkenhahn 1 , C. Fladerer1, K. H. Glatting 1 , S. Suhai1 and A. Hotz-Wagenblatt1 1DKFZ, German Cancer Research Center, Division of Molecular Biophysics, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany and 2Department of Computer Science and Artificial Intelligence, ETSII University of Granada, C/Daniel Saucedo Aranda s/n 18071, Granada, Spain Received January 31, 2007; Revised April 4, 2007; Accepted April 25, 2007 ABSTRACT The wealth of transcript information that has been made publicly available in recent years has led to large pools of individual web sites offering access to bioinformatics software. However, finding out which services exist, what they can or cannot do, how to use them and how to feed results from one service to the next one in the right format can be very time and resource consuming, especially for non-experts. Automating this task, we present a suite of protein annotation pipelines (tasks) developed at the German Cancer Research Centre (DKFZ) oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep). The aim of these tasks is to perform an exhaustive structural and functional analysis employing a wide variety of methods in combination with the most updated public databases. The three servers are available for academic users at the HUSAR open server http:// genius.embnet.dkfz-heidelberg.de/menu/biounit/ open-husar/ INTRODUCTION As more and more genomes are automatically sequenced, comprehensive protein annotation is a needed step after gene identiﬁcation. Even in good annotated genomes (human, mouse) about 30% of all proteins are not functionally identiﬁed (1–3), and thus often a similarity search will not be suﬃcient. Here, we present a suite of protein tasks, ProtSweep, DomainSweep and 2Dsweep, which perform analysis from sequence similarity to small domains and structural elements. This includes similarity searches against protein sequence databases and special- ized motif collections, prediction of secondary structural elements, attributing each sequence to known super- families, protein localization prediction, physicochemical protein characteristics and domain functional assignation. Our strategy for assigning relevant functional roles is based on the joint use of both global (homology similarity) and local (domain and motif) sequence similarities (4). The three servers are available for academic users at the HUSAR open server http://genius. embnet.dkfz-heidelberg.de/menu/biounit/open-husar/ WEB INTERFACE The input for all the three servers is a protein sequence. Several query sequences can be uploaded by the usual ‘copy & paste’ procedure into the input box using FASTA format. If more than one sequence is to be queried, a multiple FASTA ﬁle can be used. The query starts by clicking on the ‘submit’ button. Then the user will be redirected to an application page, and the run‘‘ button can start the task. Additionally, there is a link to an online help, indicated with a ‘?’, with the following topics: short description, programs employed, algorithm, output, additional options and acknowledgments. Results can be received by selecting the tab ‘Go to results page’. The results are provided as HTML for visual inspection or can be downloaded as XML for storage in private databases. In case of error when clicking on the application name in the Results Manager page, a log-ﬁle is displayed where more human readable error messages can be found. Databases Standard protein databases used by the tasks like Uniprot/SwissProt, Uniprot/TREMBL and RefSeq are automatically updated whenever new versions become *To whom correspondence should be addressed. Tel: þ49-6221-422349; Fax: þ49-6221-439633; Email: c.delval@dkfz.de, delval@decsai.ugr.as Present address: M. Falkenhann, Sanofi-Aventis Deutschland GmbH, Germany C. Fladerer, Proteom Centrum Tu¨ bingen, Germany 2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.