SUMMARY Numerous metagenomics projects have produced tremendous amounts of sequencing data. Aligning these sequences to reference genomes is an essential analysis in metagenomics studies. Large-scale alignment data call for intuitive and efficient visualization tool. However, current tools such as various genome browsers are highly specialized to handle intraspecies mapping results. They are no...

SUMMARY The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements...

Parallel text alignment is a key procedure in the automated translation area. A large number of aligners have been presented along the years, but these require that the target resources have been pre-prepared for alignment (either manually or automatically). It is rather normal to encounter mixed language documents, that is, documents where the same information is written in many languages (Ex:...

Yawat 1 is a tool for the visualization and manipulation of wordand phrase-level alignments of parallel text. Unlike most other tools for manual word alignment, it relies on dynamic markup to visualize alignment relations, that is, markup is shown and hidden depending on the current mouse position. This reduces the visual complexity of the visualization and allows the annotator to focus on one ...

MOTIVATION A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new alignment approach (Slider) that reduces the alignment problem space by utilizing each...

Progressive sequence model refinement by means of iterative searches is an effective technique for high sensitivity database searches and is currently employed in popular tools such as PSI-BLAST and SAM. Recently, a novel alignment algorithm has been proposed that offers features expected to improve the sensitivity of such iterative approaches, specifically a well-characterized theory of its st...

Multiple RNA structure alignment is particularly challenging because covarying mutations make sequence information alone insufficient. Many existing tools for multiple RNA alignments first generate pairwise RNA structure alignments and then build the multiple alignment using only the sequence information. Here we present PMFastR, an algorithm which iteratively uses a sequence-structure alignmen...

We propose a user-friendly automatic phonetic alignment tool for continuous speech: EasyAlign. It is developed and freely distributed as a plug-in of Praat, the popular speech analysis software. Its main advantage is that one can easily align speech from an orthographic transcription. It requires a few minor manual steps and the result is a multi-level annotation within a TextGrid composed of p...

Ontology matching and alignment is a key mechanism for linking the diverse datasets and ontologies arising in the Semantic Web. We show that category theory provides the powerful abstractions needed for a uniform treatment at various levels: semantics, language design, reasoning and tools. The Distributed Ontology Language DOL is extended in a natural way with constructs for networks of ontolog...

In this paper we describe a 3D scanning software suite which gives support to most of the processing phases of a complex 3D scanning project. In particular, our tools support: range maps alignment, range maps merge, mesh editing and mesh simplification. The software suite has been implemented by scratch and encompasses both up-to-date solutions (alignment, editing) and some original methods (me...