MZEF (Michael Zhang's Exon Finder) was designed to help identify one of the most important classes of exons, i.e. the internal coding exons, in human genomic DNA sequences. It is neither for predicting intronless genes, nor for assembling predicted exons into complete gene models. There is also a mouse version (mMZEF) and an Arabidopsis version (aMZEF). This unit presents the Unix and Web versi...

STEREO is a novel algorithm that discovers cis-regulatory RNA interactions by assembling complete and potentially overlapping same-strand RNA transcripts from tiling expression data. STEREO first identifies coherent segments of transcription and then discovers individual transcripts that are consistent with the observed segments given intensity and shape constraints. We used STEREO to identify ...

103 It is a pleasure to read and discuss Gene Grossman and Esteban Rossi-Hansberg’s paper. They begin by assembling several data series to show the growing importance of “task trade,” or offshoring, for the U. S. economy. Unfortunately, few data sets exist on offshoring, so, while highly suggestive, all the evidence is indirect. Hence, the first policy implication that I draw from this paper is...

A gene is a macromolecule which codes for the structure of a protein. Lehninger (1967) points out, "The ascent from simple self-assembling systems such as oligomeric proteins and enzyme complexes to the level of supramolecular organization of subcellular organelles is a very steep one. In making it we cross a boundary to a level of organization at which the self-assembly principle doubtless ope...

SUMMARY AnnBuilder is an R package for assembling genomic annotation data. The system currently provides parsers to process annotation data from LocusLink, Gene Ontology Consortium, and Human Gene Project and can be extended to new data sources via user defined parsers. AnnBuilder differs from other existing systems in that it provides users with unlimited ability to assemble data from user sel...

Facile, one-step synthesis of self-assembling, cationic block copolymers of poly(2-N-(dimethylaminoethyl) methacrylate) (pDMAEMA) and PEO-PPO-PEO (Pluronic®) is developed. The copolymers are obtained via free-radical polymerization of DMAEMA initiated by Pluronic-radicals generated by cerium (IV). The copolymers possess surface activity, are polycationic at pH<7.1, and self-assemble into micell...

A conceptual design for artificial antimicrobial viruses is described. The design emulates viral assembly and function to create self-assembling peptide capsules that promote efficient gene delivery and silencing in mammalian cells. Unlike viruses, however, the capsules are antimicrobial, which allows them to exhibit a dual biological function: gene transport and antimicrobial activity. Unlike ...

To date, assembling comprehensive annotation information for all probe sets of any Affymetrix microarrays remains a time-consuming, error-prone and challenging task. ChipInfo is designed for retrieving annotation information from online databases such as NetAffx and Gene Ontology and organizing such information into easily interpretable tabular format outputs. As companion software to dChip and...

A conceptual design for artificial antimicrobial viruses is described. The design emulates viral assembly and function to create self-assembling peptide capsules that promote efficient gene delivery and silencing in mammalian cells. Unlike viruses, however, the capsules are antimicrobial, which allows them to exhibit a dual biological function: gene transport and antimicrobial activity. Unlike ...