9 Result(s)

Article

DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention

Repetitive elements contribute a large part of eukaryotic genomes. For example, about 40 to 50% of human, mouse and rat genomes are repetitive. So identifying and classifying repeats is an important step in ge...

Fabian Hausmann, Stefan Kurtz in Algorithms for Molecular Biology (2021)

Article

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns

It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structu...

Fernando Meyer, Stefan Kurtz, Michael Beckstette in BMC Bioinformatics (2013)

Article

Readjoiner: a fast and memory efficient string graph-based sequence assembler

Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction ...

Giorgio Gonnella, Stefan Kurtz in BMC Bioinformatics (2012)

Article

Structator: fast index-based search for RNA sequence-structure patterns

The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence...

Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will… in BMC Bioinformatics (2011)

Article

CoCoNUT: an efficient system for the comparison and analysis of genomes

Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and so...

Mohamed I Abouelhoda, Stefan Kurtz, Enno Ohlebusch in BMC Bioinformatics (2008)

Article

Efficient computation of absent words in genomic sequences

Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on. Unique subsequences are ma...

Julia Herold, Stefan Kurtz, Robert Giegerich in BMC Bioinformatics (2008)

Article

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

Transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. While there are several completed eukaryotic g...

David Ellinghaus, Stefan Kurtz, Ute Willhoeft in BMC Bioinformatics (2008)

Article

Optimising oligonucleotide array design for ChIP-on-chip

Fiona Nielsen, Stefan Graef, **nmin Zhang, Stefan Kurtz… in BMC Bioinformatics (2007)

Article

Fast index based algorithms and software for matching position specific scoring matrices

In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching with PSSMs in complete genomes ...

Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz in BMC Bioinformatics (2006)