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 approximately 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/.
Klee
Eric W
EW
Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.
Shim
Kyong Jin
KJ
Pickart
Michael A
MA
Ekker
Stephen C
SC
Ellis
Lynda B M
LB
D017931:DNA Primers / Q000737:chemistry; D023281:Genomics / Q000379:methods*; D020407:Internet; D009025:Morpholines / Q000737:chemistry*; D016376:Oligonucleotides, Antisense / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface
D017931:DNA Primers; D009025:Morpholines; D016376:Oligonucleotides, Antisense