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The 5′- and 3′-untranslated regions (5′- and 3′-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and stability. UTRdb is a specialized database of 5′ and 3′ untranslated sequences of eukaryotic mRNAs cleaned from redundancy. UTRdb entries are enriched with specialized information not present in the primary databases including the presence of nucleotide sequence patterns already demonstrated by experimental analysis to have some functional role. All these patterns have been collected in the UTRsite database so that it is possible to search any input sequence for the presence of annotated functional motifs. Furthermore, UTRdb entries have been annotated for the presence of repetitive elements. All Internet resources we implemented for retrieval and functional analysis of 5′- and 3′-UTRs of eukaryotic mRNAs are accessible at http://bighost.area.ba.cnr.it/BIG/UTRHome/.

GeneSyn is a software tool that allows automatic detection of conserved gene order from annotated genomes. The increasing amount of available genome data makes it possible now to shed light on the molecular dynamics shaping their evolution. Genome evolution not only involves changes at the sequence level with base substitutions and/or insertion/deletion events but also rearrangements of the gene order along the genome. Comparative analysis of gene order in multiple genomes may help in investigating general or lineage-specific genome plasticity as well as in the inference of phylogenetic relationships. In particular, investigation of gene contiguity on a chromosome (sometimes improperly referred to as conserved gene synteny), even if sometimes interrupted by intervening genes, suggests a functional coupling. We present here an algorithm and software to detect gene strings conserved in at least a given fraction of input genomes and present a simple example application in animal mitochondrial gene order