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Nucleic Acids Research 2005 33(Web Server Issue):W506-W511; doi:10.1093/nar/gki453
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

AMOD: a morpholino oligonucleotide selection tool

Eric W. Klee1,4, Kyong Jin Shim3,4, Michael A. Pickart2,4, Stephen C. Ekker2,4 and Lynda B. M. Ellis1,4,*

1Department of Laboratory Medicine and Pathology, University of Minnesota Minneapolis, MN, USA 2Department of Genetics, Cell Biology and Development, University of Minnesota Minneapolis, MN, USA 3Department of Computer Science and Engineering, University of Minnesota Minneapolis, MN, USA 4Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota Minneapolis, MN, USA

*To whom correspondence should be addressed at Mayo Mail Code 609, 420 SE Delaware Street, Minneapolis, MN 55455, USA. Tel: +1 612 625 9122; Fax: +1 612 624 6404; Email: lynda{at}umn.edu

Received February 11, 2005. Revised April 1, 2005. Accepted April 1, 2005.

AMOD is a web-based program that aids in the functional evaluation of nucleotide sequences through sequence characterization and antisense morpholino oligonucleotide (target site) selection. Submitted sequences are analyzed by translation initiation site prediction algorithms and sequence-to-sequence comparisons; results are used to characterize sequence features required for morpholino design. Within a defined subsequence, base composition and homodimerization values are computed for all putative morpholino oligonucleotides. Using these properties, morpholino candidates are selected and compared with genomic and transcriptome databases with the goal to identify target-specific enriched morpholinos. AMOD has been used at the University of Minnesota to design ~200 morpholinos for a functional genomics screen in zebrafish. The AMOD web server and a tutorial are freely available to both academic and commercial users at http://www.secretomes.umn.edu/AMOD/.

Present address: Michael A. Pickart, Department of Biology, University of Wisconsin–Stout, Menomonie, Wisconsin, WI, USA


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