2001 © Ashley Publications Ltd The assembly of a multiple sequence alignment (MSA) has become one of the most common tasks when dealing with sequence analysis. Unfortunately, the wide range of available methods and the differences in the results given by these methods makes it hard for a non-specialist to decide which program is best suited for a given purpose. In this review we briefly describ...

Genome-wide computational analysis for small nuclear RNA (snRNA) genes resulted in identification of 76 and 73 putative snRNA genes from indica and japonica rice genomes, respectively. We used the basic criteria of a minimum of 70 % sequence identity to the plant snRNA gene used for genome search, presence of conserved promoter elements: TATA box, USE motif and monocot promoter specific element...

Multiple sequence alignment (MSA) is used to explore the similarity of several related protein sequences by providing a near optimal alignment of the characters in each sequence. Biologists require effective visualization of these alignments as part of their analysis. Although tools such as Jalview have been developed that provide a detailed view of different aspects of the alignments and metad...

Pseudoknots are essential for the functioning of many small RNA molecules. In addition, viral RNAs often exhibit pseudoknots that are required at various stages of the viral life-cycle. Techniques for detecting evolutionarily conserved, and hence most likely functional RNA pseudoknots, are therefore of interest. Here we present an extension of the alidot approach that extracts conserved seconda...

Sequence alignment is an important task in bioinformatics which involves typical database search where data is in the form of DNA, RNA or protein sequence. For alignment various methods have been devised starting from pairwise alignment to multiple sequence alignment (MSA). To perform multiple sequence alignment various methods exists like progressive, iterative and concepts of dynamic programm...

Multiple sequence alignment is a central problem in Bioinformatics and a challenging one for optimisation algorithms. An established integer programming approach is to apply branch-and-cut to a graph-theoretical model. The models are exponentially large but are represented intensionally, and violated constraints can be located in polynomial time. This report describes a new integer program form...