Expressed sequence tags (ESTs) are partial cDNA sequences read from both ends of random expressed gene fragments used for discovering new genes. DNA libraries from four different developmental stages of Schistosoma mansoni used in this study generated 141 ESTs representing about 2.5% of S. mansoni sequences in dbEST. Sequencing was done by the dideoxy chain termination method. The sequences wer...

How do two identical DNA sequences find each other during homologous recombination, amidst a 'sea' of unrelated DNA? New studies reveal how RecA promotes the search for homology by sampling DNA in three dimensions.

Since the demonstration that the sequence of a protein encodes its structure, the prediction of structure from sequence remains an outstanding problem that impacts numerous scientific disciplines, including many genome projects. By iteratively fixing secondary structure assignments of residues during Monte Carlo simulations of folding, our coarse-grained model without information concerning hom...

Biological sequence similarity analysis presents visualization challenges, primarily because of the massive amounts of discrete, multi-dimensional data. Genomic data generated by molecular biologists is analyzed by algorithms that search for similarity to known sequences in large genomic databases. The output from these algorithms can be several thousand pages of text, and is difficult to analy...

One of the problems arising in the analysis of biological sequences is the discovery of sequence similarity by finding common motifs. Several versions of the motif finding problem have been proposed for dealing with this problem and for each version, numerous algorithms have been developed. In this paper, we propose an exact algorithm, called SMS-H-FORBID to solve the Simple Motif Problem (SMP)...

Genomic sequence databases are widely used by molecular biologists for homology searching Amino acid and nucleotide databases are increasing in size exponentially and mean sequence lengths are also increasing In searching such databases it is desirable to use heuristics to perform computationally intensive local alignments on selected sequences only and to reduce the costs of the alignments tha...

BACKGROUND The basic molecular mechanisms that govern the search for DNA homology and subsequent homologous pairing during genetic recombination are not understood. RecA is the central homologous recombination protein of Escherichia coli; because several RecA homologues have been identified in eukaryotic cells, it is likely that the mechanisms employed by RecA are conserved throughout evolution...

Pairing of homologous chromosomes during early meiosis is essential to prevent the formation of aneuploid gametes. Chromosome pairing includes a step of homology search followed by the stabilization of homolog interactions by the synaptonemal complex (SC). These events coincide with dramatic changes in nuclear organization and rapid chromosome movements that depend on cytoskeletal motors and ar...

In the last years, a number of semantic biomedical systems have been developed to store biomedical knowledge in an accessible manner. However, their practical usage is limited, since they require expertise in semantic languages by the user, or, in the other hand, their query interfaces do not fully exploit the semantics of the knowledge represented. Such drawbacks were present in the OGO system...