Probabilities of all possible correspondences of residues in aligning two proteins are evaluated by assuming that the statistical weight of each alignment is proportional to the exponent of its total similarity score. Based on such probabilities, a probability alignment that includes the most probable correspondences is proposed. In the case of highly similar sequence pairs, the probability ali...

Relating ontologies is very important for many ontology-based applications and more important in open environments like the semantic web. The relations between ontology entities can be obtained by ontology matching and represented as alignments. Hence, alignments must be taken into account in ontology management. This chapter establishes the requirements for alignment management. After a brief ...

The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archae...

The goal of instance matching is to detect identity resources, which refer to the same real-world object. In this paper, we introduce SLINT+, a novel interlinking system. SLINT+ detects all identity linked data resources between two given repositories. SLINT+ does not require the specifications of RDF predicates and labeled matching resources. SLINT+ performs competitively at OAEI instance matc...

In this study we apply and evaluate an iterative pairwise alignment program for producing multiple sequence alignments, ALPHAMALIG (Alonso et al., 2004), using as material the phonetic transcriptions of words used in Bulgarian dialectological research. To evaluate the quality of the multiple alignment, we propose two new methods based on comparing each column in the obtained alignments with the...

S4 is an automatically generated database of multiple structure-based sequence alignments of protein superfamilies in the SCOP database. All structural domains that do not share more than 40% sequence identity as defined by the ASTRAL compendium of protein structures are included. The alignments are constructed using pairwise structural alignments to generate residue equivalences that are then ...

s on Human Factors in Computing Systems, Minneapolis, MN, April 20 25, 2002, New York, NY: ACM, pp. 574 575, 2002. H. Martin and B. Gaver, ‘‘Beyond the snapshot from speculation to prototypes in audiophotography’’, in Proceedings of the 3rd Conference on Designing Interactive Systems: Processes, Practices, Methods, and Techniques (DIS’00), New York City, NY, August 17 19, 2000, D. Boyarski and ...

We propose a simple approach to visual alignment, focusing on the illustrative task of facial landmark estimation. While most prior work treats this as a regression problem, we instead formulate it as a discrete K-way classification task, where a classifier is trained to return one of K discrete alignments. One crucial benefit of a classifier is the ability to report back a (softmax) distributi...

We present a multiple genome alignment browser for sequences from numerous multiple alignments. Our goal is to use information visualization to help users think about how sequences have evolved over time. Our application takes as input a series of multiple alignments in MAF format and outputs an interactive visual display of the data. 1 Information visualization Information visualization has in...