Beschreibung:
<jats:title>Summary</jats:title><jats:sec><jats:label /><jats:p>
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<jats:list-item><jats:p>Terminal restriction fragment length polymorphism (<jats:styled-content style="fixed-case">TRFLP</jats:styled-content>) analysis remains a useful technique to obtain insights into the genetic diversity of microbial populations. A crucial parameter of the technique is the selection of appropriate restriction endonucleases (<jats:styled-content style="fixed-case">RE</jats:styled-content>s) to achieve high resolution between the <jats:styled-content style="fixed-case">PCR</jats:styled-content>‐amplified fragments of a marker gene (usually a ribosomal <jats:styled-content style="fixed-case">RNA</jats:styled-content> gene). However, despite the development of several computer‐supported programmes to improve the selection of <jats:styled-content style="fixed-case">RE</jats:styled-content>s for <jats:styled-content style="fixed-case">TRFLP</jats:styled-content> analysis, there is still a lack of software that offers both of two aspects: first, availability of a sequence data base from which sequences can easily and without further formatting and ranking be selected for analysis; secondly, selection of sets of <jats:styled-content style="fixed-case">RE</jats:styled-content>s for highest genetic resolution while providing the possibility to assess and quantify the correlation of the <jats:styled-content style="fixed-case">TRF</jats:styled-content>s with the phylogeny of the target group of 16<jats:styled-content style="fixed-case">S</jats:styled-content> r<jats:styled-content style="fixed-case">RNA</jats:styled-content> sequences.</jats:p></jats:list-item>
<jats:list-item><jats:p>Here, we present a new and freely available software tool which utilises ARB in combination with the <jats:sc>silva</jats:sc> data base of hundreds of thousands of aligned ribosomal <jats:styled-content style="fixed-case">RNA</jats:styled-content> genes or user‐submitted sequences as basis for the selection of optimal sets of <jats:styled-content style="fixed-case">RE</jats:styled-content>s of various sizes. Apart from coping with missing sequence information and providing extensive information on the obtained <jats:styled-content style="fixed-case">TRF</jats:styled-content> patterns, this new programme for <jats:italic>O</jats:italic>ptimising <jats:italic>E</jats:italic>n<jats:italic><jats:styled-content style="fixed-case">ZY</jats:styled-content></jats:italic>me selection for best performing TRFLP analysis using ARB (<jats:styled-content style="fixed-case">OEZY</jats:styled-content>) also assesses the level at which the resulting <jats:styled-content style="fixed-case">TRF</jats:styled-content> pattern reflects the phylogeny based on the data base gene sequences.</jats:p></jats:list-item>
<jats:list-item><jats:p>Optimising EnZYme is a substantial extension to hitherto available software as it opens the chance to correctly predict the phylogenetic position of yet unknown sequence types. Choosing <jats:styled-content style="fixed-case">RE</jats:styled-content>s that lead to a high correlation between the resulting <jats:styled-content style="fixed-case">TRF</jats:styled-content>s and the phylogeny of the micro‐organisms based on the nucleotide sequence of the marker gene makes it likely that the <jats:styled-content style="fixed-case">TRF</jats:styled-content>s also fall within the corresponding phylogenetic clade. <jats:styled-content style="fixed-case">OEZY</jats:styled-content> therefore provides a diagnostic tool for the analysis of microbial populations.</jats:p></jats:list-item>
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