Title

AMOD: a morpholino oligonucleotide selection tool

Publication Type

Journal Article

Publication Date

2005

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 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/.

Keywords

antisense oligomers, gene knockdown, embryos, rna, translation, zebrafish, design, screen, model

Discipline

Bioinformatics | Computer Sciences

Research Areas

Intelligent Systems and Decision Analytics

Publication

Nucleic Acids Research

Volume

33

Issue

Suppl 2

First Page

W506

Last Page

W511

ISSN

0305-1048

Identifier

10.1093/nar/gki453

Publisher

Oxford University Press

Additional URL

http://dx.doi.org/10.1093/nar/gki453