Bioinformatics and Statistics Unit

Activities

The Bioinformatics and Statistics Unit in involved in both research and technological support activities.The unit is lead by Alessandra Stella, PhD. Le attività principali della sezione riguardano la bioinformatica, l'analisi statistica e l'informatica.

Research Activities:
1) design of procedures for biological sequences analysis
2) study of the genetic basis for quantitative traits of economic importance in agriculture
3) design of statistical methods and procedures
4) population genetics studies

Technological support activities:
1) statistical analysis
2) software implementation
3) database implementation
4) high performances computing

Projects

Software + Database:

Grape MiRNA DB

Two complete genome sequences are available for Vitis vinifera Pinot noir. Based on the sequence and gene predictions produced by the IASMA, we performed an in silico detection of putative microRNA genes and of their targets, and collected the most reliable microRNA predictions in a web database... (more details here)

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Human ESTs explorer

A web facility for comparison of expression levels among libraries from several healthy and diseased tissues... (more details here)

ESTree DB (versioni I, II, III, IV, V, VI)

The ESTree db (http://www.itb.cnr.it/estree) represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database... (more details here)

ESTuber DB (versioni I e II)

The ESTuber database (http://www.itb.cnr.it/estuber) includes 3,271 Tuber borchii expressed sequence tags (EST). The dataset consists of 2,389 sequences from an in-house prepared cDNA library from truffle vegetative hyphae, and 882 sequences downloaded from GenBank and representing four libraries from white truffle mycelia and ascocarps at different developmental stages. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts. Data were collected in a MySQL database, which can be queried via a php-based web interface... (more details here)

GoSh DB

The GoSh database is a collection of 58 990 Capra hircus and Ovis aries expressed sequence tags. A perl pipeline was prepared to process sequences, and data were collected in a MySQL database. A PHP-based web interface allows browsing and querying the database. Putative single nucleotide polymorphism (SNP) detection... (more details here)

Sturgeon DB

The Sturgeon DB is a collection of expressed sequence tags (EST) from Acipenser transmontanus, Ictalurus punctatus, Salmo salar and Takifugu rubripes skin and spleen non-normalized libraries.

Bovine SNP Retriever

Online resources for the bovine genome analysis are provided at the most important Web sites. Nonetheless, retrieval of single-nucleotide polymorphism (SNP)-related information is not always easy when searches must focus on complementary features. In this work, we present the Bovine SNP Retriever: a user-friendly tool for bovine SNP retrieval that also facilities the retrieval of SNP-related information within user-selected quantitative traits loci regions and reverse electronic polymerase chain reaction analysis on the bovine genome... (more details here)

Misagen

Misagen DB is a database of environmental, genetic and health-related data information of a commercial swine population in Northern Italy.

Eurigen

"Genotyping for the Conservation and Valorization of European Rice Germplasm", is a project financed by the European Commission - DG Agriculture and Rural Development within the AGRI GEN RES program for conservation, characterisation, collection and utilization of genetic resources in agriculture.

HAPROB (software download)

An algorithm and a software to estimate haplotype probabilities for genotyped members of half-sib families for which parents lacked genotypic information... (more details here)

Collaborations

LITBIO: Laboratory for Interdisciplinary Technologies in Bioinformatics
CNR-ITB: National Research Council - Institute for Biomedical Technologies
CNR-IBBA: Institute of Agricultural Biology and Biotechnology
VSA - Department of Veterinary Sciences and Technology for Food Safety of the University of Milan
Università Cattolica del Sacro Cuore di Piacenza-Cremona