Microarrays are widely used with the aim to identifing the overall effects of experimental conditons on the gene expression profile at trascription level. A challenging question related with the use of microarrays is the enormous amount of information generated in multifactorial experiments. To this aim we developed a web accessible system to store, analyze and retrieve microarray data.

Multiple alignments of protein sequences are important tools in studying sequences. The basic information they provide is identification of conserved sequence regions. This is very useful in designing experiments to test and modify the function of specific proteins, in predicting the function and structure of proteins, and in identifying new members of protein families. Sequences can be aligned across their entire length (global alignment) or only in certain regions (local alignment).

Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT's speed stems from an index of all nonoverlapping K-mers in the genome.

Blast stands for Basic Local Alignment Search Tool. The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of this novel sequence.

Biological risk management requires effective identification and typing of microbial species to support prompt public health decisions. Several molecular strategies are valuable, but sequence based methods currently represent a best suitable approach. Traditional culture-based techniques are often inadequate or inapplicable in environmental microbiology or epidemiology studies. Molecular procedures involving sequencing of amplification products are essential, but result storage and analysis is still complex and needs appropriate bioinformatics tools to exploit data exchange and comparison real time. To provide an online user-friendly tool for the everyday practice of the operator involved in retrieving nucleic acid sequences for monitoring bacteria transmission routes, we designed a GENetically-based system for typing ENVironmental microrganisms: GenEnv.