UNLABELLED Interactive examination of RNA multiple alignments for covariant mutations is a useful step in non-coding RNA sequence analysis. We present three parallel implementations of an RNA visualization metaphor: Colorstock, a command-line script using ANSI terminal color; SScolor, a Perl script that generates static HTML pages; and Ratón, an AJAX web application generating dynamic HTML. Eac...

We introduce a new graph-based multiple sequence alignment method for protein sequences. We name our method HSA (Horizontal Sequence Alignment) for it horizontally slides a window on the protein sequences simultaneously. Current progressive alignment tools build up final alignment by adding sequences one by one to existing alignment. Thus, they have the shortcoming of order-dependent alignment....

Lexical-Functional Grammar (LFG) fstructures (Kaplan and Bresnan, 1982) have attracted some attention in recent years as an intermediate data representation for statistical machine translation. So far, however, there are no alignment tools capable of aligning f-structures directly, and plain word alignment tools are used for this purpose. In this way no use is made of the structural information...

To date, few tools for aligning protein-protein interaction networks have been suggested. These tools typically find conserved interaction patterns using various local or global alignment algorithms. However, the improvement of the speed, scalability, simplification, and accuracy of network alignment tools is still the target of new researches. In this paper, we introduce Pin-Align, a new tool ...