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/.
Bibliographical noteFunding Information:
The authors thank Michelle Knowlton, Aidas Nasevicius and Eric Mendenhall, for providing valuable feedback on AMOD’s function and user interface. Vanessa Louis, 2004 University of Minnesota undergraduate Bioinformatics Summer Intern (NSF/NIBIB EEC-0234112), assisted with analysis of relationships between phenotypic outcomes and sequence characteristics. This work was supported in part by NIH R01-GM63904, a predoctoral traineeship to E.K. (NLM TG-0704l), and a postdoctoral traineeship to M.A.P. (NIDCR: T32 DE07288-8). Funding to pay the Open Access publication charges for this article was provided by NIH R01-GM 63904.