AMOD: a morpholino oligonucleotide selection tool
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 similar to 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/.
antisense oligomers, gene knockdown, embryos, rna, translation, zebrafish, design, screen, model
Bioinformatics | Computer Sciences
Intelligent Systems and Decision Analytics
Nucleic Acids Research
Oxford University Press
KLEE, Eric W.; SHIM, Kyong Jin; Pickart, Michael A.; Ekker, Stephen C.; and Ellis, Lynda B. M..
AMOD: a morpholino oligonucleotide selection tool. (2005). Nucleic Acids Research. 33, (Suppl 2), W506-W511. Research Collection School Of Information Systems.
Available at: http://ink.library.smu.edu.sg/sis_research/1507