AMOD: a morpholino oligonucleotide selection tool

• Main Authors: KLEE, Eric W., SHIM, Kyong Jin, Pickart, Michael A., Ekker, Stephen C., Ellis, Lynda B. M.
• Format: text
• Language: English
• Published: Institutional Knowledge at Singapore Management University 2005
• Subjects: antisense oligomers; gene knockdown; embryos; rna; translation; zebrafish; design; screen; model; Bioinformatics; Computer Sciences
• Online Access: https://ink.library.smu.edu.sg/sis_research/1507; http://dx.doi.org/10.1093/nar/gki453
• Institution: Singapore Management University

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/.