Cover illustration: A cladogram presention of omptin protein sequence alignment.

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...

Some sequence-comparison methods also try to include secondary and tertiary structural information. Because different secondary structural elements can be formed from very similar segments of sequence (see section 4-14), using structural information in the description of the reference protein could, in theory at least, help exclude proteins with somewhat similar sequences but very different str...

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 In recent years, several methods have been proposed for aligning two protein sequence profiles, with reported improvements in alignment accuracy and homolog discrimination versus sequence-sequence methods (e.g. BLAST) and profile-sequence methods (e.g. PSI-BLAST). Profile-profile alignment is also the iterated step in progressive multiple sequence alignment algorithms such as CLUSTAL...

Motivation: In recent years, several methods have been proposed for aligning two protein sequence profiles, with reported improvements in alignment accuracy and homolog discrimination versus sequence-sequence methods (e.g. BLAST) and profile-sequence methods (e.g. PSIBLAST). Profile-profile alignment is also the iterated step in progressive multiple sequence alignment algorithms such as CLUSTAL...

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...

MOTIVATION Alignment of RNA has a wide range of applications, for example in phylogeny inference, consensus structure prediction and homology searches. Yet aligning structural or non-coding RNAs (ncRNAs) correctly is notoriously difficult as these RNA sequences may evolve by compensatory mutations, which maintain base pairing but destroy sequence homology. Ideally, alignment programs would take...

One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple sequence alignment has been proposed. Two different genetic operators mainly c...

One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple sequence alignment has been proposed. Two different genetic operators mainly c...