Bioinformatics Tools for the analysis of data from "omics" studies

by the Laboratory of Bioinformatics and Computational Biology, ISA - CNR, Italy

Welcome to our web pages and tools for bioinformatics analysis of data generated by "omics" studies.

This activity of the Lab is supported by the InterOmics Flagship Project. The Lab is involved in the development of bioinformatics tools to help partners of the Program in the analysis of experimental data from oncoproteomics studies.

Here, we present the tools we developed with the Project, and previous tools of interest for this field.

For any comment, suggestions, request, please send an e-mail to angelo.facchiano (at)


ALI-SPECTRA is designed to align signals from mass spectra, to verify the presence of common peaks as well as to highlight specific signals.


NEAPOLIS offers a quick an robust procedure to align signals from mass spectra, with different features in comparison to ALI-SPECTRA.


PROTEIN_FINDER accepts a list of protein accession numbers and analyzes features of the sequences, such as amino acid composition, number of observable peptides, and others.


LIST_COMP is designed to compare two lists of accession numbers, or other codes, and to highlight duplications of lists, shared and unique codes.


PROSCAN is a tool to search patterns within a given protein sequence, and performs composition analysis.


HELM is a software developed to search for HELix Motifs within protein sequences.



ASC is a collection of active sequences of peptides, useful to search for similarities of a given sequence with proteins segments and peptides with a biological activity.


GALT is a database with structural and functional information about GALT enzyme and its known mutant forms.

Other tools coming soon ...


[1] Mangerini R, Romano P, Facchiano A, Damonte G, Muselli M, Rocco M, Boccardo F, Profumo A. (2011) The application of atmospheric pressure matrix-assisted laser desorption/ionization to the analysis of long-term cryopreserved serum peptidome. Anal Biochem. 417, 174-181. PubMed link
[2] Facchiano AM, Facchiano A, Facchiano F. (2003) Active Sequences Collection (ASC) database: a new tool to assign functions to protein sequences. Nucleic Acids Res. 31, 379-382. PubMed link
[3] Facchiano AM. (2000) HELM: searching for helix motifs within protein sequences. Bioinformatics 16, 292-293. PubMed link
[4] Marabotti A, Facchiano AM. (2005) Homology modeling studies on human galactose-1-phosphate uridylyltransferase and on its galactosemia-related mutant Q188R provide an explanation of molecular effects of the mutation on homo- and heterodimers. J Med Chem. 48, 773-779. PubMed link
[6] d'Acierno A, Facchiano A, Marabotti A. (2009) GALT protein database, a bioinformatics resource for the management and analysis of structural features of a galactosemia-related protein and its mutants. Genomics Proteomics Bioinformatics 7, 71-76. PubMed link
[7] Facchiano A, Marabotti A. (2010) Analysis of galactosemia-linked mutations of GALT enzyme using a computational biology approach. Protein Eng Des Sel. 23, 103-113. PubMed link
[8] Tang M, Facchiano A, Rachamadugu R, Calderon F, Mao R, Milanesi L, Marabotti A, Lai K. (2012) Correlation assessment among clinical phenotypes, expression analysis and molecular modeling of 14 novel variations in the human galactose-1-phosphate uridylyltransferase gene. Hum Mutat 33, 1107-1115. PubMed link
[9] Boutron A, Marabotti A, Facchiano A, Cheillan D, Zater M, Oliveira C, Costa C, Labrune P, Brivet M; French Galactosemia Working Group. (2012) Mutation spectrum in the French cohort of galactosemic patients and structural simulation of 27 novel missense variations. Mol Genet Metab. 2012 Aug 6. [Epub ahead of print] PubMed link