BACKGROUND The Smith-Waterman algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools for next-generation sequencing data. Though various fast Smith-Waterman implementations are developed, they are either designed as monolithic protein database searching tools, which do not...

A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view o...

MOTIVATION Owing to recent advancements in high-throughput technologies, protein-protein interaction networks of more and more species become available in public databases. The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology. Network alignments provide a systematic way to solve this problem. However, most existing a...

In biological and biomedical research motif finding tools are important in locating regulatory elements in DNA sequences. There are many such motif finding tools available, which often yield position weight matrices and significance indicators. These indicators, p-values and E-values, describe the likelihood that a motif alignment is generated by the background process, and the expected number ...

Multiple Sequence Alignment (MSA) is essential for a wide range of applications in Bioinformatics. Traditionally, the alignment accuracy was the main metric used to evaluate the goodness of MSA tools. However, with the growth of sequencing data, other features, such as performance and the capacity to align larger datasets, are gaining strength. To achieve these new requirements, without affecti...

This article focuses on the key step of obtaining the best possible sequence alignment of the Query (the protein you are interested in) to the Target (a protein of known three-dimensional structure) in order to build a molecular model for molecular replacement. Common sequence-alignment methods are discussed, starting from structural alignment and then moving to pairwise, multiple and profile-p...

We present first results of a track based alignment procedure applied to test beam data recorded with Cosmic Rack, a test setup which mimicks the outer barrel of the CMS Tracker. The Hits and Impact Points alignment method is used within the CMS reconstruction software framework to align this telescope-like device. These results were compared to results obtained with manual alignment and to res...

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...

With the increase of genome and proteome data, phylogenetic information and phylogenetic analysis tools are increasing greatly in current biological repositories. First, many repositories allow users to browse information about species through taxonomic tools. These tools present the species with its lineage path and links to the various types of information the repository provides about the sp...

Multiple sequence alignment (MSA) is used to align three or more sequences of DNA, RNA and protein. It prominent for constructing phylogenetic trees evolutionary relationships between with regard similarities dissimilarities. Variety multiple tools are available online, each having different methods parameters sequences. In this article MSA tools; CLUSTALW, SAGA MAFFT five datasets BALiBASE_R9,...