In the world of RNAs and proteins, similarities at the level of primary structures of two comparable molecules usually correspond to structural similarities at the tertiary level. In other words, measures of sequence and structure similarities are in general correlated - a high value of sequence similarity imposes a high value of structural similarity. However, important exceptions that stay in...

The information analyses of RNA sequences on the basis of their secondary structures have been rapidly advanced these few years. We briefly review the basic concepts related with RNA sequence analyses and introduce our contributions to recent progress in structural alignments of RNA sequences.

Accuracy of predicting protein secondary structure and solvent accessibility has been improved significantly by using evolutionary information contained in multiple sequence alignments. For the second Asilomar meeting, predictions were made automatically for all targets using the publicly available prediction service PredictProtein. Additionally, a semiautomatic procedure for generating more in...

The play-in/play-out approach is a method for specifying and developing complex reactive systems. It is built upon a scenariobased philosophy, and uses the language of live sequence charts (LSCs) and a support tool called the Play-Engine. We present some conclusions from the initial experience we have had using the approach on several projects, and discuss methodological aspects rising from thi...

On the basis of mitochondrial DNA sequence analyses, Thangaraj et al. (Brevia, 13 May 2005, p. 996) proposed that Andaman islanders descended from the first humans to migrate out of Africa. We identified mitochondrial DNA from two northeast Indian Rajbanshi individuals that shares three specific mutations with the M31a lineage observed in the Great Andamanese, which suggests that the predecesso...

Correct alignment of the sequence of a target protein with those of homologues of known three-dimensional structure is a key step in comparative modeling. Usually an iterative approach that takes account of the local and overall structural features is required. We describe such an approach that exploits databases of structural alignments of homologous proteins (HOMSTRAD, http:/(/)www-cryst.bioc...

The genome projects have unearthed an enormous diversity of genes of unknown function that are still awaiting biological and biochemical characterization. These genes, as most others, can be grouped into families based on sequence similarity. The PFAM database currently contains over 2,200 such families, referred to as domains of unknown function (DUF). In a coordinated effort, the four large-s...

1. In a sub-tropical epidemic, most of the apparent household secondary cases are actually secondary infections. 2. The consensus sequence for the entire influenza virus genome is not usually identical within the same household sample. Rather, there are commonly one or two nucleotide changes. 3. These results hint at an obvious generational threshold for adaptation at the level of the consensus...

Using information from sequence alignments significantly improves protein secondary structure prediction. Typically, more divergent profiles yield better predictions. Recently, various groups have shown that accuracy can be improved significantly by using PSI-BLAST profiles to develop new prediction methods. Here, we focused on the influences of various alignment strategies on two 8-year-old PH...