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Comparative and Functional GenomicsComp Funct Genom 2002; 3: 397.Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.210
In this issue
Upstream — news in genomics
In this issue we report on important papers pub-lished from May to July, highlighting break-throughs on several important genomes, includ-ing mouse, zebrafish, Fugu and Plasmodium.Other recent papers have reported on a mech-anism for genome size reduction in Arabidop-sis, comparisons and verifications of large-scaleprotein-protein interaction datasets, developmentsin RNA interference approaches for mammaliansystems and a solid-phase peptide tagging methodfor proteomics.
A mathematical analysis of suppressionsubtraction hybridisation
Chetan Gadgil et al. present a mathematical modelof SSH based on DNA hybridization kinetics. Theyhave used their model to assess the effects of vari-ous experimental parameters (such as mRNA abun-dance in the cDNA sample and the reaction timeused) on the chances of detecting messages fromdifferent abundance classes, and on the number offalse positives obtained, to facilitate optimisationof the approach. They also use the model to lookat the best way to spike a sequence into the drivercDNA pool.
A computational strategy for proteinfunction assignment that deals with thedomain problem
Antonio Perez and colleagues describe and demon-strate an automated approach to protein functionclassification that combines the keyword (KW) andfeature (FT) fields of SWISS-PROT entries to buildup a database of protomotifs. When a novel pro-tein shows similarity to an annotated protein, thefunctional information from a protomotif is onlytransferred to the novel protein if the match is inthe correct region of the protein.
Meeting Review: ESF — Impact of nucleicacid chemistry on gene function analysis
Kathrin Heermeier et al. report on the ESF pro-gramme on Integrated Approaches for FunctionalGenomics workshop “Impact of Nucleic AcidChemistry on Gene Function Analysis: Antisense,Aptamers, Ribozymes and RNAi”.
Meeting Review: From genotype tophenotype: Linking Bioinformatics andMedical Informatics Ontologies
In first of two reports from Manchester Bioinfor-matics Week, Ele Holloway reviews the ontologiesworkshop that launched the conference. The talkscovered issues in nomenclature and data standardsand profiled a range of existing ontologies andprojects currently in development.
Meeting Review: CCP11 Group Meeting:Towards the Functional Analysis ofMicroarrays
Clare Sansom reports on the CCP11 group microar-ray analysis meeting from Manchester Bioinfor-matics Week. The meeting focussed mainly onstatistical methods and analysis, with some presen-tations on modelling of networks, and profiles of aselection of microarray projects.
Meeting Review: The 50th AmericanSociety for Mass Spectrometry meeting
Francesco Brancia brings us a report from theannual meeting of the ASMS: ‘Mass Spectrometryand Allied Topics’. The development of new massspectrometers and implementation of new analyt-ical methods were the central themes of the con-ference, and, as last year, the application of massspectrometry to proteomics was a hot topic.
Copyright 2002 John Wiley & Sons, Ltd.
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