This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions between all pairs of input sequences are iteratively estimated in TurboFold II ...

Pattern matching techniques have been useful in solving many problems associated with computer science, including data compression (Chrochemore and Lecroq, 1996), data encryption (RSA Laboratories, 1993), and computer vision (Grimson and Huttenlocher, 1990). In recent years, developments in molecular biology have led to large scale sequencing of genomic DNA. Since this data is being produced in...

The Freiburg RNA tools web server integrates three tools for the advanced analysis of RNA in a common web-based user interface. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively. The Freiburg RNA tools web server and the software packages of the stand-alone tools are freely accessible at http://rna.informa...

9 In the last decade a number of algorithms and associated software have been 10 developed to align next generation sequencing (NGS) reads with relevant 11 reference genomes. The accuracy of these programs may vary significantly, 12 especially when the NGS reads are quite different from the available reference 13 genome. We propose a benchmark to assess accuracy of short reads mapping 14 based ...

Three are many stand-alone tools available for Bioinformatics. This package aims at using R and the Biostrings package as the common interface for several important tools for multiple sequence alignment (clustalw, kalign), classification (RDP), sequence retrieval (BLAST) as well as database driven sequence management for 16S rRNA.

Pairwise sequence alignment is ubiquitous in modern bioinformatics. It may be performed either explicitly, e.g. to find the most similar sequences in a database, or implicitly as a hidden building block of more complex methods, e.g. for reads mapping. The alignment algorithms have been widely investigated over the last few years, mainly with respect to their speed. However, no attention was giv...

MOTIVATION The amplified interest in metabolic profiling has generated the need for additional tools to assist in the rapid analysis of complex data sets. RESULTS A new program; metabolomics spectral formatting, alignment and conversion tools, (MSFACTs) is described here for the automated import, reformatting, alignment, and export of large chromatographic data sets to allow more rapid visual...

As networks are typically formed by heterogeneous and autonomous entities, it is natural that each member has its own set of values. As a result, the ability to quickly identify partners with compatible or common values represents an important element for the success of collaborative networks. However, tools to measure the level of alignment are lacking. Applying some soft modeling tools, this ...

Comparative analysis of protein networks has proven to be a powerful approach for elucidating network structure and predicting protein function and interaction. A fundamental challenge for the success of this approach is the development of efficient algorithms and tools for comparing multiple networks. In this thesis we present two novel tools for comparative network analysis. The first tool is...

The rapid increase in the use of metabolite profiling/fingerprinting techniques to resolve complicated issues in metabolomics has stimulated demand for data processing techniques, such as alignment, to extract detailed information. In this study, a new and automated method was developed to correct the retention time shift of high-dimensional and high-throughput data sets. Information from the t...