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38. Rother K, Preissner R, Goede A, Froemmel C: Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins. Bioinformatics 2003, 19:2112–2121.PubMedCrossRef Authors’ contributions MO conceived of the study, carried out the molecular genetic #selleck compound randurls[1|1|,|CHEM1|]# studies, participated in the design of the study and drafted the manuscript. AG, MN and MM carried out the molecular genetic studies. MW performed homology modeling of TmaSSB and EcoSSB. JK participated in design of study and drafted the manuscript. All authors read and approved the final manuscript.”
“Background Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis of 16S rRNA gene amplicons is a rapid fingerprinting method for characterization of microbial communities [1, 2]. It is based on the restriction endonuclease digestion profile of fluorescently end-labeled PCR products. The digested products are separated by capillary gel electrophoresis, detected and registered on an automated sequence analyzer. Each T-RF is represented by a peak in the output chromatogram and corresponds to members of the community that share a given terminal fragment size. Peak area is proportional to the abundance of the Milciclib in vivo T-RF in the PCR amplicon

pool, which can be used as a proxy for relative abundance in natural populations [3]. This method is rapid, relatively inexpensive and provides distinct profiles that reflect the taxonomic composition of sampled communities. Although it has extensively been used for comparative purposes, a T-RFLP fingerprint alone does not allow for conclusive taxonomic identification of individual phylotypes because it is technically challenging to recover terminal fragments for direct sequencing. However, when coupled with sequence data for representative 16S rRNA genes, T-RF identification is feasible (e.g. [4–6]). Here we describe

a method to assign the T-RF peaks generated by T-RFLP analysis with either 16S rRNA gene sequences obtained from clone libraries Liothyronine Sodium of the same samples, metagenome sequences or data from public 16S rRNA sequence databases. T-RFPred can thus be used to classify T-RFs from T-RFLP profiles for which reference clone libraries are not available, albeit with lower phylogenetic resolution, by taking advantage of the wealth of 16S rRNA gene sequence data available from metagenome studies and public databases such as the Ribosomal Database Project (RDP) [7] or SILVA [8]. Metagenome sequencing studies from a variety of environments are accumulating at a rapid pace. While most often partial gene sequences, these libraries have the advantage that they are less subject to biases of other PCR-based techniques (see e. g. [9] for a review) and, thus, can better represent the original community structure.