Michael Sammeth

Publications of Michael Sammeth

• Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms.

  Authors: Alexander Mellmann, Thomas Weniger, Christoph Berssenbrügge, Jörg Rothgänger, Michael Sammeth, Jens Stoye, Dag Harmsen

  BMC microbiology. 02/2007; 7:98.

  BACKGROUND: For typing of Staphylococcus aureus, DNA sequencing of the repeat region of the protein A (spa) gene is a well established discriminatory method for outbreak investigations. Recently, itBACKGROUND: For typing of Staphylococcus aureus, DNA sequencing of the repeat region of the protein A (spa) gene is a well established discriminatory method for outbreak investigations. Recently, it was hypothesized that this region also reflects long-term epidemiology. However, no automated and objective algorithm existed to cluster different repeat regions. In this study, the Based Upon Repeat Pattern (BURP) implementation that is a heuristic variant of the newly described EDSI algorithm was investigated to infer the clonal relatedness of different spa types.For calibration of BURP parameters, 400 representative S. aureus strains with different spa types were characterized by MLST and clustered using eBURST as "gold standard" for their phylogeny. Typing concordance analysis between eBURST and BURP clustering (spa-CC) were performed using all possible BURP parameters to determine their optimal combination. BURP was subsequently evaluated with a strain collection reflecting the breadth of diversity of S. aureus (JCM 2002; 40:4544). RESULTS: In total, the 400 strains exhibited 122 different MLST types. eBURST grouped them into 23 clonal complexes (CC; 354 isolates) and 33 singletons (46 isolates). BURP clustering of spa types using all possible parameter combinations and subsequent comparison with eBURST CCs resulted in concordances ranging from 8.2 to 96.2%. However, 96.2% concordance was reached only if spa types shorter than 8 repeats were excluded, which resulted in 37% excluded spa types. Therefore, the optimal combination of the BURP parameters was "exclude spa types shorter than 5 repeats" and "cluster spa types into spa-CC if cost distances are less than 4" exhibiting 95.3% concordance to eBURST. This algorithm identified 24 spa-CCs, 40 singletons, and excluded only 7.8% spa types. Analyzing the natural population with these parameters, the comparison of whole-genome micro-array groupings (at the level of 0.31 Pearson correlation index) and spa-CCs gave a concordance of 87.1%; BURP spa-CCs vs. manually grouped spa types resulted in 95.7% concordance. CONCLUSION: BURP is the first automated and objective tool to infer clonal relatedness from spa repeat regions. It is able to extract an evolutionary signal rather congruent to MLST and micro-array data.

• Global multiple-sequence alignment with repeats.

  Authors: Michael Sammeth, Jaap Heringa

  Proteins. 08/2006; 64(1):263-74.

  Repeating fragments in biological sequences are often essential for structure and function. Over the years, many methods have been developed to recognize repeats or to multiply align proteinRepeating fragments in biological sequences are often essential for structure and function. Over the years, many methods have been developed to recognize repeats or to multiply align protein sequences. However, the integration of these two methodologies has been largely unexplored to date. Here, we present a new method capable of globally aligning multiple input sequences under the constraints of a given repeat analysis. The method supports different stringency modes to adapt to various levels of detail and reliability of the repeat information available.

• Panta rhei (QAlign2): an open graphical environment for sequence analysis.

  Authors: Michael Sammeth, Thasso Griebel, Felix Tille, Jens Stoye

  Bioinformatics (Oxford, England). 05/2006; 22(7):889-90.

  MOTIVATION: The first version of the graphical multiple sequence alignment environment QAlign was published in 2003. Heavy response from the molecular-biological user community clearly demonstratedMOTIVATION: The first version of the graphical multiple sequence alignment environment QAlign was published in 2003. Heavy response from the molecular-biological user community clearly demonstrated the need for such a platform. RESULTS: Panta rhei extends QAlign by several features. Major redesigns on the user interface, for instance, allow users to flexibily compose views for multiple projects. The new sequence viewer handles datasets with arbitrarily many and arbitrarily large sequences that may still be edited by guided block moving. More distance-based algorithms are available to interactively reconstruct phylogenetic trees which can now also be zoomed and navigated graphicaly. AVAILABILITY: Executables and the JAVA source code are available under the Apache license at http://gi.cebitec.uni-bielefeld.de/qalign CONTACT: qalign@cebitec.uni-bielefeld.de.

• net.researchgate.refind.jaxb.schema.dblp.I@3ca83cdd

  Authors: Michael Sammeth, Thasso Griebel, Felix Tille, Jens Stoye

  Bioinformatics. 01/2006; 22:889-890.

• Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI).

  Authors: Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye

  Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings; 01/2005

• RIDOM: comprehensive and public sequence database for identification of Mycobacterium species.

  Authors: Dag Harmsen, Stefan Dostal, Andreas Roth, Stefan Niemann, Jörg Rothgänger, Michael Sammeth, Jürgen Albert, Matthias Frosch, Elvira Richter

  BMC infectious diseases. 12/2003; 3:26.

  BACKGROUND: Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The informationBACKGROUND: Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The information content of the 5' end of the 16S ribosomal RNA gene (16S rDNA) is sufficient for identification of most bacterial species. However, reliable sequence-based identification is hampered by many faulty and some missing sequence entries in publicly accessible databases. METHODS: In order to establish an improved 16S rDNA sequence database for the identification of clinical and environmental isolates, we sequenced both strands of the 5' end of 16S rDNA (Escherichia coli positions 54 to 510) from 199 mycobacterial culture collection isolates. All validly described species (n = 89; up to March 21, 2000) and nearly all published sequevar variants were included. If the 16S rDNA sequences were not discriminatory, the internal transcribed spacer (ITS) region sequences (n = 84) were also determined. RESULTS: Using 5'-16S rDNA sequencing a total of 64 different mycobacterial species (71.9%) could be identified. With the additional input of the ITS sequence, a further 16 species or subspecies could be differentiated. Only Mycobacterium tuberculosis complex species, M. marinum/M. ulcerans and the M. avium subspecies could not be differentiated using 5'-16S rDNA or ITS sequencing. A total of 77 culture collection strain sequences, exhibiting an overlap of at least 80% and identical by strain number to the isolates used in this study, were found in the GenBank. Comparing these with our sequences revealed that an average of 4.31 nucleotide differences (SD +/- 0.57) were present. CONCLUSIONS: The data from this analysis show that it is possible to differentiate most mycobacterial species by sequence analysis of partial 16S rDNA. The high-quality sequences reported here, together with ancillary information (e.g., taxonomic, medical), are available in a public database, which is currently being expanded in the RIDOM project http://www.ridom-rdna.de), for similarity searches.

• Divide-and-conquer multiple alignment with segment-based constraints.

  Authors: Michael Sammeth, Burkhard Morgenstern, Jens Stoye

  Bioinformatics (Oxford, England). 11/2003; 19 Suppl 2:ii189-95.

  A large number of methods for multiple sequence alignment are currently available. Recent benchmarking tests demonstrated that strengths and drawbacks of these methods differ substantially. GlobalA large number of methods for multiple sequence alignment are currently available. Recent benchmarking tests demonstrated that strengths and drawbacks of these methods differ substantially. Global strategies can be outperformed by approaches based on local similarities and vice versa, depending on the characteristics of the input sequences. In recent years, mixed approaches that include both global and local features have shown promising results. Herein, we introduce a new algorithm for multiple sequence alignment that integrates the global divide-and-conquer approach with the local segment-based approach, thereby combining the strengths of those two strategies.

• Digital extractor: analysis of digital differential display output.

  Authors: Michael Sammeth, Jörg Rothgänger, W. Esser, Jürgen Albert, Jens Stoye, Dag Harmsen

  Bioinformatics. 01/2003; 19:1592-1593.

• Comparing Tandem Repeats with Duplications and Excisions of Variable Degree

  Authors: Michael Sammeth, Jens Stoye

  IEEE/ACM Transactions on Computational Biology and Bioinformatics. 3:395-407.

• Alignment of tandem repeats with excision, duplication, substitution and indels (EDSI)

  Authors: Michael Sammeth, Jens Stoye

  Traditional sequence comparison by alignment applies a mutation model comprising two events, substitutions and indels (insertions or deletions) of single positions (SI). However, modern geneticTraditional sequence comparison by alignment applies a mutation model comprising two events, substitutions and indels (insertions or deletions) of single positions (SI). However, modern genetic analysis knows a variety of more complex mutation events (e.g., duplications, excisions and rearrangements), especially regarding DNA. With the ever more DNA sequence data becoming available, the need to accurately compare sequences which have clearly undergone more complicated types of mutational processes is becoming critical. Herein we introduce a new model, where in total four mutational events are considered: excision and duplication of tandem repeats, as well as substitutions and indels of single positions (EDSI). Assuming the EDSI model, we develop a new algorithm for pairwisely aligning and comparing DNA sequences containing tandem repeats. To evaluate our method, we apply it to the spa VNTR (variable number of tandem repeats) of Staphylococcus aureus, a bacterium of great medical importance.

• Comparing tandem repeats with duplications and excisions of variable degree.

  Authors: Michael Sammeth, Jens Stoye

  IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM. 3(4):395-407.

  Traditional sequence comparison by alignment employs a mutation model comprised of two events, substitutions and indels (insertions or deletions) of single positions. However, modern genetic analysisTraditional sequence comparison by alignment employs a mutation model comprised of two events, substitutions and indels (insertions or deletions) of single positions. However, modern genetic analysis knows a variety of more complex mutation events (e.g., duplications, excisions, and rearrangements), especially regarding DNA. With ever more DNA sequence data becoming available, the need to accurately compare sequences which have clearly undergone more complicated types of mutational processes is becoming critical. Herein we introduce a new method for pairwise alignment and comparison of sequences with respect to the special evolution of tandem repeats: substitutions and indels of single positions and, additionally, duplications and excisions of variable degree (i.e., of one or more repeat copies simultaneously) are taken into account. To evaluate our method, we apply it to the spa VNTR (variable number of tandem repeats) cluster of Staphylococcus aureus, a bacterium of high medical importance.

• QAlign: quality-based multiple alignments with dynamic phylogenetic analysis

  Authors: Michael Sammeth, Jörg Rothgänger, Wolfram Eßer, Jürgen Albert, Jens Stoye, Dag Harmsen

  Bioinformatics, 19(12), pp. 1592-1593.

  Integrating different alignment strategies, a layout editor and tools deriving phylogenetic trees in a 'multiple alignment environment' helps to investigate and enhance results of multiple sequenceIntegrating different alignment strategies, a layout editor and tools deriving phylogenetic trees in a 'multiple alignment environment' helps to investigate and enhance results of multiple sequence alignment by hand. QAlign combines algorithms for fast progressive and accurate simultaneous multiple alignment with a versatile editor and a dynamic phylogenetic analysis in a convenient graphical user interface.