TOOLS     

ANALISI DI SEQUENZA
RNA
PROTEINE
PROTOCOLLI
PCR
SOFTWAREs
LINKAGE
SNPs
COPY NUMBER VARIANTS
METHYLATION
MOTORI DI RICERCA
FARMACOGENETICA
VARIE
STATISTICA

ANALISI  DI SEQUENZA
Sequence Format Converter
GEECEE (Calculates the fractional GC content of a nucleic acid sequence)

TANDEM REPEATS FINDER (a public database of tandem repeats that allows users to run their own sequences)
RepeatMasker (RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences)
ECR Browser (a dynamic whole-genome navigation tool for visualizing and studying evolutionary relationships between vertebrate and non-vertebrate genomes)
PDA - Pipeline Diversity Analysis (A tool to explore and estimate nucleotide diversity in DNA databases)
UCSC ( This site contains the reference sequence and working draft assemblies for a large collection of genomes)

Alignment
VSNS BioComputing Division Multiple Alignment Resource page
CLUSTALW
BLAST2 (This tool produces the alignment of two given sequences using BLAST engine for local alignment )
BLAST
BLAT (molto più veloce di BLAST!!!)
ABIM Online analysis tools (Search sequence databases, Alignment)
                    VISTA (VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own                                         sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species)

Gene structures (promoter prediction, transcription factors, transcription start sites)
CBS (Center for Biological  Sequence Analysis)
BioBencHelper (Databases, Tools & Softwares)
BIMAS Signal Scan (Find and list homologies of published signal sequences with the input DNA sequence)
New GENSCAN Web Server at MIT (Identification of complete gene structures in genomic DNA)
Biocenter Helsinky (Link Collection about nucleic acid sequence analysis)
WWW Signal Scan (Find and list homologies of published signal sequences with the input DNA sequence)
SOFTBERRY (Gene. Operon, Promoter.... finding,  Multiple alignments, and much more!)
The CpG Island Searcher
DNA Motif and StructureTools (Gene finders, Motifs indentification, ORF and promoter search, Transcription factors binding sites search)
BDGP (Berkeley Drosophila Genome Project - Enter a DNA sequence to find possible transcription promoters)
CorePromoter (Core Promoter Prediction Program)
BIMAS Proscan (Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences)
cisRED ( The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations)
BIOBASE (Transfac, Transpath, Links.....)
DEAMBULUM (Gene structure prediction, ORFs, specific sites)
TESS (Transcription Element Search System)
MAPPER (an online resource for exploring transcription factor binding sites in H. sapiens, M. musculus, and D. Melanogaster) 
DBTSS Database of transcriptional start sites (full length cDNAs! gives information about Potential Alternative Promoters!) 
DCODE (Comparative Genomics Center is a publicly available resourse for regulatory genome data mining. It provides tools for evolutionary comparisons, sequence alignments, and detection of functional sequence patterns.)

                    Restriction analysis

REBsites (fa analisi di restrizione e mostra pattern atteso su gel di agarosio a varie concentrazioni)
NEBcutter V2.0 (New England Biolabs - DNA restriction sites finder)
Restriction Analysis
WatCut (An on-line tool for restriction analysis, silent mutation scanning, and SNP-RFLP analysis)
In silico simulation of molecular biology experiments
Restriction Enzyme Resource
DNA Tools  (A collection of methods which graphically represent various DNA parameters)

RNA
RegRNA (A Regulatory RNA motifs and elements finder)
POLYAH (Recognition of 3'-end cleavage and polyadenilation region)
UTResource (
UTResource collect data and analysis tool for the functional classification of 5' and 3'UTRs of eukaryotic mRNAs)
UTRdb
TransTerm (an interactive database providing access to mRNA sequences and associated regulatory elements)
The RNA World Web Site (This web resource lists Internet links on RNA related topics)
GUTELL Lab Comparative RNA Web Site
Transcript DoTS (Database Of Transcibed Sequences - human and mouse)
IFTI-MIRAGE Website (Molecular Informatics Resource for the Analysis of Gene Expression)
RNAdb (mammalian noncoding RNA database)
microRNA
miRNA registry
TDL_miRBase (miRNA predetti  analizzando sequenze introniche e EST non coding)
NATsDB (Natural Antisense Transcripts DataBase)

Splicing
GilAstLab (ESRsearch, Analyzer Splice Tool, Branch Site Tool)
ESE Finder (Exonic Splicing Enhancers (ESEs))
RESCUE-ESE web server
PESXs (Putative Exonic Splicing Enhancers/Silencers)

MaxEntScan (to score 5' or 3' splice site)
Gene Finding and Intron Splice Site Prediction
GeneSplicer
BDGP Splice Site Prediction by Neural Network
ASPIC (Alternative Splicing PredICtion)
SpliceInfo (an information repository for mRNA alternative splicing in human genome)
Alternative splicing Database Project (Splice variants from annotated genes for human)
EuSplice (
is a unique resource which provides reliable splice signal and alternative splicing information for 23 eukaryotic genomes)
ASAP (Alternative Splicing Annotation Project EST-based splice variant prediction with tissue information)
ProSplicer (Putative alternative splice variant database for human)
SpliceMiner (a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis)
Alternative Splicing Gallery
ASePCR (Alternative Splicing electronic RT-PCR in multiple tissues and organs)
SPLICY (GeneChip Splice Machine;
a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data)
ASESdb
Useful Links to Alternative Splicing Resources
Alternative Splicing Isoform Signature
fast DB (the Friendly Alternative Splicing and Transcripts Database)
ASTD (Alternative Splicing and Transcript Diversity)

H-DBAS (
Human-transcriptome DataBase for Alternative Splicing)

PROTEINE
Pedro's BioMolecular Research Tools (A collection of WWW Links to Information and Services Useful to Molecular Biologists)
PDB (The RCSB Protein Data Bank)
Macromolecular Structure Database (EMBL)
NPD (Nuclear Protein Database)
EMP (Enzymes and Metabolic Pathways Database)
METABOLISM
KEGG (Kyoto Encyclopedia of Genes and Genomes.Database on metabolic and regulatory pathways including graphical schemas)
ModBase (a database of three-dimensional protein models calculated by comparative modeling) (per predizione dell'effetto di SNP su struttura proteica)
BindN (
prediction of DNA and RNA binding residues in proteins)
MAISTAS (
Modeling and Assessment of ISoforms Through Automated Server)

PROTOCOLLI
NWFSC Molecular Biology Protocols
Cell Biology Laboratory Manual
Protocols - Bioinformatics.Net
PROTOCOL ON LINE (Molecular Biology/Protein Protocols)
MOLECULAR CLONING (Maniatis on line manual)
Protocolli
TUFTS University (Laboratory Protocols)
Cell & Molecular Biology Online (Methods and Protocols)
Protocol Online: Molecular Biology/Protein Protocols
JoVE (Journal of Visualized Experiments)

PCR
Pedro's BioMolecular Research Tools (A collection of WWW Links to Information and Services Useful to Molecular Biologists)
PCR Jump Station
Primo (PCR primer design tools)
PCR Primer Design (links collection)
Primer Design (Primer Prediction and Alnalysis Programs)
Design PCR Primers
PCR Primer Selection (sequence input:  from Genbank or direct entry)
Tavi's PCR Protocols (PCR and multiplex PCR: guide and troubleshooting)
PCR (Troubleshooting, Help, Suggestions and Advice)
ExonPrimer ( ExonPrimer is a Perl script that helps to design intronic primers for the PCR amplification of exons)
ExPrimer (A novel tool to design primer from exon-junctions)
PCR optimization
PCR primer design links
OligoCalc (oligonucleotide Properties Calculator)
PCR Box Titration Calculator
In silico simulation of molecular biology experiments
MethPrimer is a program for designing bisulfite-conversion-based Methylation PCR Primers
OligoAnalyzer
(hairpins, self & hetero dimers)

Real Time PCR
Real Time PCR Tutorial
(molto chiaro)
Real-Time PCR Tutorial (by T. Dorak)
Real Time PCR Handbook
qPCR Technical Guide (SIGMA)
www.Gene-Quantification (esaustivo)
qPCR Info Portal (geNorm, qBase, BestKeeper... downloads / statistical analysis ...)
RealTime Protocols
qPCRforum.com
(Discuss GenEx  and qPCR)
free qPCR design software (an online qpcr design tool that can be used to screen SYBR® Green primers and TaqMan® probes for possible secondary structures such as dimers or hairpins)

SOFTWAREs
Genetics Software Archive (Genetics and Molecular Biology Software for the PC)
Laboratory Tools (A collection of software tools for streamling the daily activities associated with life science bench research- STRATAGENE)
ImageJ (Image Processing and Analysis in Java)
PHASE (a Software Package for PHylogenetics And Sequence Evolution)

LINKAGE
Functional Genomics (Complex Disease Trait Mapping, Genome Mapping, Linkage Analysis)
Genetic Linkage Analysis (at Rockefeller University)
Genetic Linkage (tutorial)
Quantitative Genetics (tutorial)
CEPH Genotype Database

SNPs
dbSNP (NCBI)
Human Genome Variation Society Databases
SNPper
MutationDiscovery (Nucleotide Variation and Mutation Database)
NIEHS (National Institute of Environmental Health  Sciences)
Hapmap (The HapMap is a catalog of common genetic variants. It describes what these variants are, where they occur in our DNA, and how they are distributed  among people within populations and among populations in different parts of the world)
1000 Genomes (A Deep Catalog of Human Genetic Variation. The goal of the 1000 Genomes Project is to find most genetic variants that have frequencies of at least 1% in the populations               studied.)
Genome Variation Server (A comprehensive database that provides quick access to all data found in both the dbSNP and HapMap databases. The database includes a suite of analysis tools          such as linkage disequilibrium plots, tag SNPs, merging populations, and more. In addition you can upload our own data and use the GVS analysis and visualization tools)
Variome.net (openfree web resource and encyclopedia for world wide SNP researchers)
General mutations and polymorphysms

SNP function prediction
          PupaSNP Finder (a web tool for finding SNPs with putative effect at transcriptional level)
         
SIMP (SNP Information Mining Pipeline)
 
         RegSNP (Predicting Allele Specific Differences in Transcription Factor - DNA binding)
          SNP Inspector (Identify TF sites affected by SNPs)
          is-rSNP (in silico regulatory SNP detection)
          SNPnexus (SNPnexus was designed to simplify and assist in the selection of functionally relevant Single Nucleotide Polymorphisms)
          SNP2NMD (a database of human SNPs causing nonsense-mediated mRNA decay)
         
          Genome-Wide Association Studies (GWAs)         

         
A Catalog of Published Genome-Wide Association Studies
          HuGe Navigator (HuGE Navigator provides access to a continuously updated knowledge base in human genome epidemiology, including information on population prevalence of genetic                           variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests)
          Genetic Association Database (The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders)


        COPY NUMBER VARIANTS
                    Database of genomic variants (
A curated catalogue of large-scale variation in the human genome.)


        METHYLATON
                    Catalogue of Parent of Origin Effects

                    MethPrimer is a program for designing bisulfite-conversion-based Methylation PCR Primers
                    Epigenetics BioForum
                    BioQ Analyzer (a software tool for easy visualization and quality control of DNA methylation data from bisulfite sequencing)
                    Meth BLAST (
a sequence similarity search program designed to explore in silico bisulfite modified DNA)
                    Bi Search (
It may be used for both bisulfite converted as well as for original not modified sequences)
                    DBPC (Bisulfite sequencing Data Presentation and Compilation)

MOTORI DI RICERCA
SCIRUS for scientific information only
MedMiner (The MedMiner combines the GeneCards and PubMed search engines)
BioNetBook (BioNetBook is a directory of web pages for biology)

FARMACOGENETICA
PharmGKB (The Pharmacogenetics and Pharmacogenomics Knowledge Base)
TUFTS University (a collection of Pharmacogenetic links)
Drug ADME - Protein associated database (serves as a resource for comprehensive information about proteins potentially
responsible for pharmacogenetic effects of pharmacokinetic origin)
PAC db (
a database for cell-based pharmacogenomics)


up
VARIE
GeneCards
Ensembl
NCBI
GeneTests
Pedro's BioMolecular Research Tools (A collection of WWW Links to Information and Services Useful to Molecular Biologists)
HUGO Gene Nomenclature
Marshfield Medical Research Foundation (Center for Medical Genetics)
Genetic Association Database (The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders)
Human Genome Mutation Database
RELNET (Finding genes and phenotypes that are more related to one another)
PSEUDOGENE.org (Human, Mouse, Worm, Fly, Yeast Pseudogenes Database)
i2b2 (Informatics for Integrating Biology and the Bedside)
TeleThon Genetic Biobank Network (biological samples and related clinical data from individuals affected by genetic diseases, from their relatives or from healthy control individuals)
Recommendations for the description of protein sequence variants
Database of human type I and type III collagen mutations
Computational Biology Research Center (Software & DataBase)
Gravità Zero (blog di divulgazione scientifica)
e-Mouse Atlas (
EMA: A 3-D anatomical atlas of mouse embryo development, EMAGE: the e-Mouse Atlas of Gene Expression)
Conversione volume
Web Tools Thermo scientific (primer design, restriction analysis, reaction setup calculators, biochemical conversions... )

            STATISTICA
                    Quaderno di epidemiologia
                   
R (The R project for statistical computing)