BIOINFORMATICS WEB TOOLS


BBMRI Project Web Site

 

DESCRIPTION:

A pan-European Biobanking Research Infrastructure, building on existing infrastructures, resources and technologies, specifically complemented with innovative components and properly embedded into European ethical, legal and societal frameworks. BBMRI will contribute to increase the scientific excellence and efficacy of European research in the biomedical sciences as well as expand and secure competitiveness of European research and industry in a global context.


 


Dupomics Site Logo

DESCRIPTION:

The advent of the sequencing era has opened new frontiers for plant genomics. Several organisms have been already sequenced and others, including important crop plants, are underway. In this context the Italian Ministry of Agriculture (MiPAAF) sponsored the national project "DRUPOMICS" with the aim of joining the International initiative, leaded by US Institutions, in the sequencing of the peach genome. Fourteen scientific Italian Institutions collaborate to this project.


 


 

 G2SBC Database


DESCRIPTION:

The G2SBC Database is a bioinformatics resource that collects information about genes, proteins and mathematical models related to breast cancer and provides a number of tools to analyze integrated data. Taking advantage from the multi-level approach, that is the consideration of both the "building-blocks" level (genes and proteins) and the systems level (molecular and cellular systems), the G2SBC Database enables predictions and new hypothesis formulation.

http://www.itb.cnr.it/breastcancer


 


 

Bovine SNP Site Logo


DESCRIPTION:

The Bovine SNP Retriever is intended to provide an easy retrieval system for bovine SNPs and related information.

Three main interfaces are provided:

BLAST: to blast user's sequence(s) against the bovine 3.1 Genome Assembly and retrieve SNPs contained in significant blast hits. SNP search : to search bovine SNPs according to different criteria. SNPs in user-selected QTL traits are also retrievable from this facility (please allow cookies in your browser to open links to QLT pages). Reverse e-PCR: to perform re-PCR against the bovine 3.1 Genome Assembly and retrieve SNPs contained in the amplified region.

All outputs are extensively linked to internal and external related resources.

http://www.itb.cnr.it/bovine_snp_retriever


 


Cell Cycle Site Logo


DESCRIPTION:

The Cell Cycle database is a biological resource that collects the most relevant information related to genes and proteins involved in human and yeast cell cycle processes. The database has been developed in a systems biology context, since it also stores the cell cycle mathematical models published in the recent years, with the possibility to simulate them directly. The aim of our resource is to give an exhaustive view of the cell cycle process starting from its building-blocks, genes and proteins, toward the pathway they create, represented by the models.

http://www.itb.cnr.it/cellcycle/


 


SNP Lims Site Logo


DESCRIPTION:

An information system mainly devoted to the storage and management of SNP genotype data produced by the Illumina platform from the raw outputs of genotyping into a relational database.

https://snplims.itb.cnr.it/dblims


 


 Network Italiano per l'Analisi Dati NGS Site Logo


DESCRIPTION:

The Italian NGS Data Analysis Network will connect Next Generation Sequencing technology users and data analysis providers on national level orienting its activity to the recommendations of the COST ACTION BM1006.

http://engine.ba.itb.cnr.it/


 

 


EnvHealth Web Application Logo


DESCRIPTION:

Qualitative representation of air quality, understood as the concentration of PM, and the index of associated risks. The site allows you to see through heatmap the qualitative trend of seasonal factors at play in determining the index of risk: PM, AOD, Hmix. It is also possible to observe the measurements taken from monitoring stations on the ground of ARPA Lombardia.

http://envhealth.itb.cnr.it


 


Estree Site Logo


DESCRIPTION:

ESTree is an Interuniversitary Centre of several research units in Italy devoted to the implementation of genomics and functional genomics in peach. ESTree DB is a collection of Prunus persica and Prunus amygdalus EST sequences. Sequenced clones belong to twelve peach libraries and three almond libraries produced in nine different labs.

http://www.itb.cnr.it/estree


 


GrapeMirna Site Logo


DESCRIPTION:

GrapeMiRNA is a database of in silico microRNA predictions on the Vitis vinifera Pinot noir genome produced at the Istituto Agrario di San Michele all'Adige (IASMA).

Predictions included in the database were obtained with the FindMiRNA software.

Selection of most reliable predictions was based on values of nine parameters distinctive of microRNAs.

Thresholds for the adopted parameters are based on values displayed by grape microRNAs that are available at miRBase.

The aim of the GrapeMiRNA database is to provide a set of candidate microRNAs for in vitro validation, as well as to allow inspecting genes of interest for potential microRNA target sites.

http://www.itb.cnr.it/grapemirna


 


Gosh DB Site Logo


DESCRIPTION:

The GoSh DB is a collection of 58,990 Capra hircus and Ovis aries EST sequences.

The GoSh dataset:

Ovis aries:

58,353 Ovis aries EST sequences were downloaded from GenBank and added to GoSh.

All Ovis aries sequence names in the database begin with 'Oa'.

Capra hircus:

637 Capra hircus EST sequences were downloaded from GenBank and added to GoSh.

All Capra hircus sequence names in the database begin with 'Ch'.

http://www.itb.cnr.it/gosh


 


GPU_BSM Logo


DESCRIPTION:

Cytosine DNA methylation is a stable epigenetic mark that plays a very important role in many biological processes, and is often responsible of phenotypic expressions. Bisulfite treatment of DNA is acknowledge as the gold standard technique to study methylation. Mapping bisulfite-treated reads to a reference genome represents a significant computational challenge. GPU-BSM (GPU-BiSulpite reads Mapping) is a tool able to detect methyled cytosines and to estimate the methylation level.
Based on SOAP3, GPU-BSM exploits the computational power of modern GPUs. GPU-BSM outperforms most of the cutting-edge solutions in terms of unique best mapped reads, while keeping computational time reasonably low. GPU-BSM can align reads generated with both methylC-seq and BS-seq protocols.

DOWNLOAD PAGE


 


G-SNPM Logo


DESCRIPTION:

G-SNPM is a tool that maps a short sequence (read) representative of a SNP against a reference DNA sequence in order to find the absolute position of the SNP. In G-SNPM each SNP is mapped by means an automatic three stage pipeline.

DOWNLOAD PAGE


 


KinWeb Site Logo


DESCRIPTION:

Kinweb is a collection of protein kinases encoded in the human genome. The site provides a comprehensive analysis of functional domains of each gene product. For each kinase, GenBank RefSeq and the SwissProt entry names are available along with information about kinase classification (Hanks and Hunter classification).

http://www.itb.cnr.it/kinweb


 


MitoDrome database Site Logo


DESCRIPTION:

The MitoDrome database has been developed with the aim to annotate the complete set of Drosophila melanogaster nuclear genes encoding for mitochondrial proteins [Nucleic Acids Res. (2003), 31:322-4] in order to contribute to their functional characterization. The data collected in MitoDrome derive from the comparison of Human mitochondrial proteins available in SWISSPROT vs. the Drosophila genome, ESTs and cDNA sequences available in the FlyBase database. According to the results, each Drosophila gene sharing significant homology with a human mitochondrial protein was classified as a putative Drosophila mitochondrial gene and annotated in MitoDrome.

http://mitodrome.ba.itb.cnr.it/


 


MitoRes Site Logo


DESCRIPTION:

MitoRes, is a comprehensive and reliable resource for massive extraction of sequences and sub-sequences of nuclear genes and encoded products targeting mitochondria in metazoa. It has been developed for supporting high-throughput in-silico analyses aimed to studies of functional genomics related to mitochondrial biogenesis, metabolism and to their pathological dysfunctions.

http://mitores.ba.itb.cnr.it/


 


My MIR Site Logo


DESCRIPTION:

MyMir system performs meta-predictions based on intagration, filtering and re-ranking of outputs produced by TargetScan, RNAHybrid, miRanda, Pictar, DIANA-microT, PITA. MyMir allows: to predict miRNA::target duplexes starting by miRNAs, targets or short RNA sequences (new potential miRNAs); to go deeper in miRNAs functional
characterization by investigating Gene Ontology annotations, involvement in KEGG pathways, miRNA expression, correlation with diseases, interactions with transcription factors

http://www.itb.cnr.it/micro/


 


Gene Nerve Database Site logo

DESCRIPTION:

The GNCDB contains a collection of genes expressed in the nervous system and provides a series of tools to facilitate the analysis and to encourage hypothesis formulation. The system capitalizes on data integration to create an added value from the publicly available data, such as the use of molecular interactions information to support gene annotations.

http://www.itb.cnr.it/gncdb


 


OsteoChondroGene Site Logo


DESCRIPTION:

The investigation of biomolecular mechanisms of bone/cartilage development is crucial in understanding the onset of the osteochondral genetics diseases and supporting the development of new approaches for tissue engineering. The OsteoChondroDB employs a vertical data integration strategy to connect tissue specific information referred to diverse biomolecular levels in the field of physiological and pathological bone, and bone substitute materials.

http://www.itb.cnr.it/osteochondrogene/


 


ProCMD Site Logo


DESCRIPTION:

The ProCMD web site is addressed to researchers interested in molecular aspects of thrombophilic disease. The database integrates clinical and phenotypical descriptions with functional and structural data obtained by computational approach to help to elucidate the chain of events leading from the molecular defect to disease.

http://www.itb.cnr.it/procmd


 


p53FamTaG Site Logo


DESCRIPTION:

The p53FamilyTargetGenes database is a comprehensive and reliable resource of genome-wide search of human p53, p63 and p73 direct target genes combining in silico prediction of p53 responsive elements (p53REs) and gene expression data of microarray analysis in an isogenic cellular system. It has been developed to support and integrate high-throughput in-silico and experimental analyses and represents an important reference source of knowledge for research groups involved in the field of oncogenesis, apoptosis and cell cycle regulation.

http://p53famtag.ba.itb.cnr.it/


 


ncRNA Site Logo


DESCRIPTION:

http://ncrna.ba.itb.cnr.it/


 


PlantPIs Site Logo


DESCRIPTION:

PlantPIs is a web querying system for a database collecting plant protease inhibitors data

Protease inhibitors in plants are naturally occurring proteins that inhibit the function of endogenous and exogenous proteases

The web resource is based on a relational database, containing data of plants protease inhibitors publicly accessible, and a graphical user interface providing all the necessary browsing tools, including data export functionality

PlantPIs contains information extracted principally from MEROPS database, filtered, annotated and compared with data stored in other protein and gene public databases, using both automated techniques and domain expert evaluations

The data have been re-organized in order to allow a flexible and easy way to access stored data

http://plantpis.ba.itb.cnr.it/


 


RSS Database Site Logo

DESCRIPTION:

The RSS web site describes regional genes (V, D, J) which are flanked by Recombination Signal Sequences (RSSs) that are recognized by a group of enzymes known collectively as the VDJ recombinase. RSSs are composed of seven conserved nucleotides (a heptamer) that reside next to the gene encoding sequence followed by a spacer (containing either 12 or 23 unconserved nucleotides) followed by a conserved nonamer (9 base pairs). The RSSs are present on the 3' side (downstream) of a V region and the 5' side (upstream) of the J region. These are the sides that will be involved in the joining. Only a pair of dissimilar spacer RSSs are efficiently recombined (i.e. one with a spacer of 12 nucleotides will be recombined with one that has a spacer containing 23 nucleotides). This is known as the 12/23 rule of recombination.

http://www.itb.cnr.it/rss


 


Grid Linkage Site Logo


DESCRIPTION:

The Genetic Linkage Analysis of SNP (Single Nucleotide Polymorphism) markers permits the discovery of genetic correlations in complex diseases following their transmission through family generations. The Grid Linkage application is an On-Line facility for achieving a Whole-Genome Linkage Analysis. This is obtained distributing the computational load on the Grid operated by the European Project EGEE (Enabling Grids for E-sciencE, http://www.eu-egee.org).

http://www.itb.cnr.it/linkage


 


TMAREP Site Logo

DESCRIPTION:

TMARep is a tissue bank which provides: the possibility of inserting patient, samples and block data before storing paraffined or frozen tissues; the possibility of making queries on all public information submitted into this database, with the aim of data and tissue sharing; a RDBMS where you can store your own tma experiment data; images warehouse to allow virtual pathology development.

http://www.itb.cnr.it/tmarep


 


UTRdb Site Logo

DESCRIPTION:

UTRsite database where more specific information on the functional motifs and cross-links to interacting regulatory protein are provided. In the current update the UTR entries have been organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing.

http://utrdb.ba.itb.cnr.it/


 


UTRminer Site Logo

DESCRIPTION:

UTRminer is a CMS annotating frequent sequencial patterns (FSPs) of RNA regulatory motifs in the untranslated regions (UTRs) of mRNA in Metazoa. The aim is the extraction of implicit knowledge (relations) among UTRs sequences and UTRs regulatory motifs not explicitly reported in related databases, using data mining techniques. The idea is that of mining frequent combinations of translation regulatory motifs since their significant co-occurrences could reveal functional relationships important for the post-transcriptional control of genome expression.

http://utrminer.ba.itb.cnr.it/


 


CNR-ITB Blast tool

DESCRIPTION:

http://www.ba.itb.cnr.it/BIG/Blast/BlastUTR.html


 

 


ITB tools Logo

DESCRIPTION:

UTRscan section

UTRscan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA) sequences in order to find UTR motifs. It is able to find, in a given sequence, motifs that characterize 3'UTR and 5'UTR sequences. Such motifs are defined in the UTRSite Database, a collection of functional sequence patterns located in the 5'- or 3'-UTR sequences. The UTRsite entries describe the various regulatory elements present in UTR regions and whose functional role has been established on experimental basis. Each UTRsite entry is constucted on the basis of information reported in the literature and revised by scientists experimentally working on the functional characterization of the relevant UTR regulatory element. UTRsite database could reveal very useful for automatic annotation of anonymous sequences generated by sequencing projects as well as for finding previously undetected signals in known gene sequences.

UTRblast section

UTRblast utility allows database searches against fully annotated UTRdb entries..

http://itbtools.ba.itb.cnr.it/


 


UTRSite Logo

DESCRIPTION:

Understanding the basic mechanisms of cell growth, differentiation and response to environmental stimuli, i.e. the program controlling the temporal and spatial order of molecular events, is becoming a real challenge in molecular biology. Indeed, although most of the regulatory elements are thought to be embedded in the non-coding part of the genomes, nucleotide databases are biased by the presence of expressed sequences mostly corresponding to the protein coding portion of the genes. Among non-coding regions, the 5' and 3' untranslated regions (5'-UTR and 3'-UTR) of eukaryotic mRNAs have often been experimentally demonstrated to contain sequence elements crucial for many aspects of gene regulation and expression.

http://utrsite.ba.itb.cnr.it/


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