On the Number of Standard and of Effective Alignments (2007)
Introduction We show how to calculate the number of all possible alignments of N sequences generalizing results of Laquer [1] and Waterman [2] who solved this problem for the special case of N = 2...
Bartels,D., Kespohl,S., Albaum,S., Druke,T., Goesmann,A., Herold,J., ...
SUMMARY: We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to...
Bartels,D., Kespohl,S., Albaum,S., Druke,T., Goesmann,A., Herold,J., ...
Bartels, D., Kespohl, S., Albaum, S., Druke, T., Goesmann, A., Herold, J., ...
SUMMARY: We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to...
Correction: Benchmarking tools for the alignment of functional noncoding DNA (2004)
Pollard, DA, Bergman, CM, Stoye, J, Celniker, SE, Eisen, MB
No abstract available.
The SYSTERS Protein Family Webserver (2002)
Meinel,T., Krause,A., Stoye,J., Schmidt,A., Luz,H., Vingron,M.
The SYSTERS Protein Family Webserver (2002)
Meinel, T., Krause, A., Stoye, J., Schmidt, A., Luz, H., Vingron, M.
Common Intervals and Sorting by Reversals: A Marriage of Necessity (2002)
A. Bergeron, S. Heber, J. Stoye
This paper revisits the problem of sorting by reversals with tools developed in the context of detecting common intervals. Mixing the two approaches yields new definitions and algorithms for the...
Common intervals and sorting by reversals: a marriage of necessity (2002)
Bergeron, A., Heber, S., Stoye, J.
This paper revisits the problem of sorting by reversals with tools developed in the context of detecting common intervals. Mixing the two approaches yields new definitions and algorithms for the...
The SYSTERS protein sequence cluster set (2000)
Krause, A., Stoye, J., Vingron, M.
The SYSTERS (short for SYSTEmatic Re-Searching) protein sequence cluster set consists of the classification of all sequences from SWISS-PROT and PIR into disjoint protein family clusters and...
Efficient Implementation of Lazy Suffix Trees (1999)
R. Giegerich, S. Kurtz, J. Stoye
We present an efficient implementation of a write-only top-down construction for suffix trees. Our implementation is based on a new, space-efficient representation of suffix trees that requires only...
On the Number of Standard and of Effective Multiple Alignments (1998)
A. Dress, B. Morgenstern, J. Stoye
We study the number of all possible alignments of N sequences, N 2, for two distinct alignment concepts proposed in the literature -- standard alignments and effective alignments (consistent...
Improving the divide-andconquer approach to sum-of-pairs multiple sequence alignment (1997)
Abstract---We consider the problem of multiple sequence alignment: given k sequences of length at most n and a certain scoring function, find an alignment that minimizes the corresponding...
On Simultaneous versus Iterative Multiple Sequence Alignment (1997)
Forschungsschwerpunkt Mathematisierung, S.W. Perrey, S. W. Perrey, J. Stoye, J. Stoye, V. Moulton, ...
One of the main problems in computational biology is the construction of biologically plausible alignments for given sequence families. Many procedures have been developed for this purpose; most are...
Two Applications of the Divide & Conquer Principle in the Molecular Sciences (1997)
Forschungsschwerpunkt Mathematisierung, G. Brinkmann, S.W. Perrey, J. Stoye
In this note, two problems from the molecular sciences are addressed: the enumeration of fullerene-type isomers and the alignment of biosequences. We report on two algorithms dealing with these...
Generating Benchmarks for Multiple Sequence Alignments and Phylogenetic Reconstructions (1997)
Stoye Evers, Phylogenetic Reconstructions, J. Stoye, D. Evers, F. Meyer
hat was used in the creation process. Figure 1 sketches the creation process of a family of four sequences. Model Input Alphabet e.g. DNA, RNA, protein Root Sequence/Average Sequence Length if no...
Divide-and-Conquer Multiple Sequence Alignment (1997)
dvantage of this fact by rst dividing s1 at its midpoint ^ c1 := djs 1 j=2e and then searching for compatible positions in the other sequences. To estimate the compatibility of slicing positions c, d...
Abstract—We consider the problem of multiple sequence alignment: given k sequences of length at most n and a certain scoring function, find an alignment that minimizes the corresponding “sum of...
The SYSTERS protein sequence cluster set
Krause, A., Stoye, J., Vingron, M.
The SYSTERS (short for SYSTEmatic Re-Searching) protein sequence cluster set consists of the classification of all sequences from SWISS-PROT and PIR into disjoint protein family clusters and...
The SYSTERS protein sequence cluster set
Krause, A., Stoye, J., Vingron, M.
The SYSTERS (short for SYSTEmatic Re-Searching) protein sequence cluster set consists of the classification of all sequences from SWISS-PROT and PIR into disjoint protein family clusters and...