Both sequence alignment and motif scan are e ective sequence analysis methods, which give us clews to a function of a newly determined sequence. Sequence alignment tools like FASTA [1] and BLAST [2] search for similar sequences from a sequence database and display the similarity. Motif scan tools search for sequence patterns which are already known to have some kind of functions from a motif da...

MOTIVATION Multiple sequence alignment is a fundamental task in bioinformatics. Current tools typically form an initial alignment by merging subalignments, and then polish this alignment by repeated splitting and merging of subalignments to obtain an improved final alignment. In general this form-and-polish strategy consists of several stages, and a profusion of methods have been tried at every...

The advent of next generation sequencing (NGS) technologies have revolutionised the way biologists produce, analyse and interpret data. Although NGS platforms provide a cost-effective way to discover genome-wide variants from a single experiment, variants discovered by NGS need follow up validation due to the high error rates associated with various sequencing chemistries. Recently, whole exome...

The performance of current sentence alignment tools varies according to the to-bealigned texts. We have found existing tools unsuitable for hard-to-align parallel texts and describe an alternative alignment algorithm. The basic idea is to use machine translations of a text and BLEU as a similarity score to find reliable alignments which are used as anchor points. The gaps between these anchor p...

Numerous tools have been developed to align genomic sequences. However, their relative performance in specific applications remains poorly characterized. Alignments of protein-coding sequences typically have been benchmarked against "correct" alignments inferred from structural data. For noncoding sequences, where such independent validation is lacking, simulation provides an effective means to...

Sequence alignments form the basis for many comparative and population genomic studies. Alignment tools provide a range of accuracies dependent on the divergence between the sequences and the alignment methods. Despite widespread use, there is no standard method for assessing the accuracy of a dataset and alignment strategy after resequencing. We present a framework and tool for determining the...

An increasing demand for new language resources of recent EU members and accessing countries has in turn initiated the development of different language tools and resources, such as alignment tools and corresponding translation memories for new languages pairs. The primary goal of this paper is to provide a description of a free sentence alignment tool CorAl (Corpus Aligner), developed at the F...

MOTIVATION A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools. RESULTS We describe COBALT, a constraint based alignment tool that implements a general framework for multiple alignment of protein sequences. COBALT finds a co...

In many heritage institutes, objects are routinely described using terms from predefined vocabularies. When object collections need to be merged or linked, the question arises how those vocabularies relate. In practice it often unclear for data providers how well alignment tools will perform on their specific vocabularies. This creates a bottleneck to align vocabularies, as data providers want ...

We present two web-based, interactive tools for creating and visualizing sub-sentential alignments of parallel text. Yawat is a tool to support distributed, manual wordand phrase-alignment of parallel text through an intuitive, web-based interface. Kwipc is an interface for displaying words or bilingual word pairs in parallel, word-aligned context. A key element of the tools presented here is t...