Skip to main page content
U.S. flag

An official website of the United States government

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Jul 1;33(Web Server issue):W506-11.
doi: 10.1093/nar/gki453.

AMOD: a morpholino oligonucleotide selection tool

Eric W Klee  1 , Kyong Jin Shim, Michael A Pickart, Stephen C Ekker, Lynda B M Ellis
Affiliations

AMOD: a morpholino oligonucleotide selection tool

Eric W Klee et al. Nucleic Acids Res. .

Abstract

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/.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Process flow chart for AMOD. The program consists of six steps, encompassing two phases: target sequence characterization and morpholino selection.
Figure 2
Figure 2
Target sequence evaluation phase. (A) The 10 highest scoring alignments for a gene sequence are presented in a BLAST report and alignment summary. (B) Putative start sites identified by either method can be selected, and the TIS position highlighted in gray text in a display of the target gene sequence.
Figure 3
Figure 3
Illustrates intra-strand binding approximation from a morpholino self-to-self alignment. In this figure, the total binding score is 30: 18 from six G–C bonds and 12 from six A–T bonds.
Figure 4
Figure 4
Oligonucleotide selection phase. (A) All intra-strand binding alignments are reported, and the alignments yielding the maximum global intra-strand binding and the maximum intra-strand binding constrained to a four-base window are noted. (B) AMOD uses a second set of BLAST comparisons between select morpholinos and genomic sequences or the transcriptome to identify genes that could be targeted by the selected morpholino oligonucleotides.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Kos R., Reedy M.V., Johnson R.L., Erickson C.A. The wingedhelix transcription factor FoxD3 is important for establishing the neural crest lineage and repressing melanogenesis in avian embryos. Development. 2001;128:1467–1479. - PubMed
    1. Boonanuntanasarn S., Yoshizaki G., Takeuchi Y., Morita T., Takeuchi T. Gene knock-down in rainbow trout embryos using antisense morpholino phosphorodiamidate oligonucleotides. Mar. Biotechnol. 2002;4:256–266. - PubMed
    1. Nasevicius A., Ekker S.C. Effective targeted gene ‘knockdown’ in zebrafish. Nature Genet. 2000;26:216–220. - PubMed
    1. Mellitzer G., Hallonet M., Chen L., Ang S.L. Spatial and temporal ‘knock down’ of gene expression by electroporation of double-stranded RNA and morpholinos into early postimplantation mouse embryos. Mech. Dev. 2002;118:57–63. - PubMed
    1. Yamada L., Shoguchi E., Wada S., Kobayashi K., Mochizuki Y., Satou Y., Satoh N. Morpholino-based gene knockdown screen of novel genes with developmental function in Ciona intestinalis. Development. 2003;130:6485–6495. - PubMed

Publication types