MOTIVATION Multiple OCCurrences Analysis (Mocca) is a new method for repeat extraction. It is based on the T-Coffee package (Notredame et al., JMB, 302, 205-217, 2000). Given a sequence or a set of sequences, and a library of local alignments, Mocca extracts every segment of sequence homologous to a pre-specified master. The implementation is meant for domain hunting and makes it fast and easy ...

ISA and ICA are two web interfaces for interactive alignment of parallel texts. ISA provides an interface for automatic and manual sentence alignment. It includes cognate filters and uses structural markup to improve automatic alignment and provides intuitive tools for editing them. Alignment results can be saved to disk or sent via e-mail. ICA provides an interface to the clue aligner from the...

Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions, which all represent different possible weighting par...

UNLABELLED We have developed Look-Align, an interactive web-based viewer to display pre-computed multiple sequence alignments. Although initially developed to support the visualization needs of the maize diversity website Panzea (http://www.panzea.org), the viewer is a generic stand-alone tool that can be easily integrated into other websites. AVAILABILITY Look-Align is written in Perl using ...

Text prediction is a form of interactive machine translation that is well suited to skilled translators. In recent work it has been shown that simple statistical translation models can be applied within a usermodeling framework to improve translator productivity by over 10% in simulated results. For the sake of efficiency in making real-time predictions, these models ignore the alignment relati...

SUMMARY Nexplorer is a web-based program for interactive browsing and manipulation of character data in NEXUS format, well suited for use with alignments and trees representing families of homologous genes or proteins. Users may upload a sequence family dataset, or choose from one of several thousand already available. Nexplorer provides a flexible means to develop customized views that combine...

SUMMARY We have developed a resource, MutDB (http://mutdb.org/), to aid in determining which single nucleotide polymorphisms (SNPs) are likely to alter the function of their associated protein product. MutDB contains protein structure annotations and comparative genomic annotations for 8000 disease-associated mutations and SNPs found in the UCSC Annotated Genome and the human RefSeq gene set. M...

Linguistic alignment, such as lexical and syntactic alignment, is a universal phenomenon influencing dialogue participants in online conversations. While adaptation can occur at lexical, syntactic and pragmatic levels, relationships between alignments at multiple levels are neither theoretically nor empirically well understood. In this study, we find that community members show pragmatic alignm...

In this paper, we propose an interactive visualization called VERMONT which tackles the problem of visualizing mutations and infers their possible effects on the conservation of physicochemical and topological properties in protein families. More specifically, we visualize a set of structure-based sequence alignments and integrate several structural parameters that should aid biologists in gain...