In: S. España, M. Ivanović, M. Savić (eds.): Proceedings of the CAiSE’16 Forum at the 28th International Conference on Advanced Information Systems Engineering, Ljubljana, Slovenia, 13-17.6.2016, published at http://ceur-ws.org Abstract Information System evolution requires a well-structured Enterprise Architecture and a rigorous management. The alignment of the architecture elements according ...

MOTIVATION Structural alignment of RNA is found to be a useful computational technique for idenitfying non-coding RNAs (ncRNAs). However, existing tools do not handle structures with pseudoknots. Although algorithms exist that can handle structural alignment for different types of pseudoknots, no software tools are available and users have to determine the type of pseudoknots to select the appr...

An important component of bioinformatics research is aimed at finding evolutionary relationships among species, since it allows us to better understand various important biological functions as they emerged in these species. These tools simultaneously trace the associated evolutionary history. In this context, sequence alignment is commonly used to understand similarities among the species by c...

Multiple sequence alignment (MSA) is used to explore the similarity of several related protein sequences by providing a near optimal alignment of the characters in each sequence. Biologists require effective visualization of these alignments as part of their analysis. Although tools such as Jalview have been developed that provide a detailed view of different aspects of the alignments and metad...

SEAVIEW and PHYLO_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEAVIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO_WIN program allows phylo...

Thesaurus alignment plays an important role in realising efficient access to heterogeneous Cultural Heritage data. Current ontology alignment techniques, however, provide only limited value for such access as they consider little if any requirements from realistic use cases or application scenarios. In this paper, we focus on two real-world scenarios in a library context: thesaurus merging and ...

In this paper we describe a new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also...

Protein structure alignment is the problem of determining an assignment between the amino-acid residues of two given proteins in a way that maximizes a measure of similarity between the two superimposed protein structures. By identifying geometric similarities, structure alignment algorithms provide critical insights into protein functional similarities. Existing structure alignment tools adopt...