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Alessandro Guffanti

Publications and source records attributed to Alessandro Guffanti.

6 recordsLinked to original sources
PubMed2004

AntiHunter: searching BLAST output for EST antisense transcripts.

AntiHunter is a new web-based tool for the identification of expressed sequence tag (EST) antisense transcripts from BLAST output. In order to perform an analysis, user is required to input a genomic sequence plus an associated list of transcript names and coordinates of the genomic region (i.e. genome annotation). After masking the repeated regions (if any), program will perform a BLASTN search of the input sequence versus the selected EST database, reporting by Email the EST entries that reveal a putative antisense transcript with respect to the user supplied list.

Algorithms↗
PubMed2004

Microarray data analysis and mining.

DNA microarray is an innovative technology for obtaining information on gene function. Because it is a high-throughput method, computational tools are essential in data analysis and mining to extract the knowledge from experimental results. Filtering procedures and statistical approaches are frequently combined to identify differentially expressed genes. However, obtaining a list of differentially expressed genes is only the starting point because an important step is the integration of differential expression profiles in a biological context, which is a hot topic in data mining. In this chapter an integrated approach of filtering and statistical validation to select trustable differentially expressed genes is described together with a brief introduction on data mining focusing on the classification of co-regulated genes on the basis of their biological function.

Cluster Analysis↗
PubMed2003

Automated DNA chip annotation tables at IFOM: the importance of synchronisation and cross-referencing of sequence databases.

The increasing popularity of DNA chip technology for the study of gene expression is producing, for each experiment, a sizable quantity of numerical data to analyse and an accompanying large number of gene identifiers that should be associated with the relevant biological annotation. We describe here a website at IFOM (FIRC Institute of Molecular Oncology) where we release regularly updated annotation tables for the most used Affymetrix oligonucleotide DNA chips and for the whole Research Genetics 46K clone collection for cDNA arrays. These tables are synchronised with every new release of the mouse and human UniGene databases (NCBI; National Center for Biotechnology Information), allowing fast and easy preliminary annotation of DNA array experiments. We also report some comparative evidence about the importance of biological database synchronisation and cross-references in the process of generating annotation tables for DNA chips.

Abstracting and Indexing↗
PubMed2002

A global analysis of Caenorhabditis elegans operons.

The nematode worm Caenorhabditis elegans and its relatives are unique among animals in having operons. Operons are regulated multigene transcription units, in which polycistronic pre-messenger RNA (pre-mRNA coding for multiple peptides) is processed to monocistronic mRNAs. This occurs by 3' end formation and trans-splicing using the specialized SL2 small nuclear ribonucleoprotein particle for downstream mRNAs. Previously, the correlation between downstream location in an operon and SL2 trans-splicing has been strong, but anecdotal. Although only 28 operons have been reported, the complete sequence of the C. elegans genome reveals numerous gene clusters. To determine how many of these clusters represent operons, we probed full-genome microarrays for SL2-containing mRNAs. We found significant enrichment for about 1,200 genes, including most of a group of several hundred genes represented by complementary DNAs that contain SL2 sequence. Analysis of their genomic arrangements indicates that >90% are downstream genes, falling in 790 distinct operons. Our evidence indicates that the genome contains at least 1,000 operons, 2 8 genes long, that contain about 15% of all C. elegans genes. Numerous examples of co-transcription of genes encoding functionally related proteins are evident. Inspection of the operon list should reveal previously unknown functional relationships.

Animals↗