RNA Web Tools & Databases

Bioinformatics

• Entrez Programming Utilities (eUtils): Tools that provide access to Entrez data outside of the regular web query interface also helpful for retrieving search results for future use in another environment. Note: to submit large queries to the NCBI data base download in batch mode.
• Perl: Tutorial assumes a very basic knowledge of UNIX and concentrates on how to write basic working perl programs.
• Perl Regular Expressions: Perl will attempt to give you 10% of regular expressions you'll use 90% of the time.
• UMass Bioinformatics Portal: The BioTools site is a resource of tools for bioinformatics for the five schools of the UMass System
• NCBI BLAST: BLAST finds regions of similarity between biological sequences.
• European Bioinformatics Institute: Rfam RNA database and web resource.

RNA-specific

• RNA Central: ncRNA sequence database: A comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms. 
  
• ncRNA.org
• The mRNA Decay Resource: Sharing of information, know-how, and wisdom among researchers who study mRNA decay.
• RNA Modification Database: A comprehensive listing of post-transcriptionally modified nucleosides form RNA.
• trnadb: Compilation of tRNA sequences and tRNA genes.
• snoRNAs: Small Nucleolar RNAs (snoRNAs) from the Yeast Saccharomyces cerevisiae. A comprehensive database of S. cerevisiae H/ACA and C/D box snoRNAs, with numerous links to snoRNA and other databases.
• 3DrRNAMod: The 3D maps database allows visualization of modification sites in the five ribosome and mRNA and tRNAs for several model organisms and permits users’ construction of 3D maps for other organisms.

RNAi

• The RNAi Web: A resource center for RNA interference (RNAi) technology.
• RNAxs: A site to design potent siRNAs to knock down your gene(s) of interest. Includes all the parameters that have been shown to influence RNAi efficiency in literature.

MicroRNAs

• miRBase: Searchable database of published miRNA sequences and annotation.
• mirWIP microRNA target identification: Allows you to search for targets of conserved microRNAs in C. elegans.
• TargetScan: Prediction of microRNA targets

Nucleic Acid Folding

• RNAfold
  Will predict secondary structures of single stranded RNA or DNA sequences.
• RNAhybrid
  For finding the minimum free energy hybridization of two RNA's.
• SFold
  Software for Statistical Folding and Rational Design of Nucleic Acids.

Miscellaneous

• Comprehensive Transposon Database
  Public research domain on genetic information (DNA sequence data), as well as dissemination of databases and computer software.
• Gene Expression Omnibus (GEO) 
  Public functional genomics data repository supporting MIAME-compliant data submissions.
• PDB Protein Databank
  PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.
• Sequence Read Archive (SRA)
  Stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helico , Heliscope, and others.
• UCSB Genome Browser
  The reference sequence and working draft assemblies for a large collection of genomes. Also a portal to the ENCODE project.

Model Organisms

• Flybase
  Database of Drosophila and genes and genomes.
• Bloomington Drosophilia Stock Center
  BDSC collects, maintains, and distributes Drosophilia melanogaster strains for research.
• Wormbase
  The biology and genome of C.elegens.
• KYOTO Stock Center (DGRC)
  Drosophila Genetic Resource Center, in KYOTO Japan, collects, maintains and supplies genetic stocks Drosophila melanogaster to Drosophila researchers worldwide.
• Vienna Drosophila RNAi Center (VDRC)
  Maintains and distributes transgenic RNAi stocks constructed by Dickson and Keleman groups at the IMP.  GD and KK collections covering a total 13,264 Drosophila genes.

UMass Chan Core Facilities

Highlighted Cores

• UMass Medical School Deep Sequencing Core: Microarray technology to analyze complex genetic data. Access to Affymetrix, Nimblegen Hybridization, and Agilent microarray scanning.
• UMass Medical School Flow Cytometry Core: Measuring the physical and chemical characteristics of cells or other biological particles.
• UMass Center for AIDS Research (CFAR) - Molecular Biology Core & Virology Core: Discounted reagents, DNA & RNA Oligos, Plasmids, Probes, Bioinformatics Resource, DNA fragment analysis, BiaCore SPR, Next Generation Deep Sequencing
• RNAi Core Facility: UMass Chan has purchased the complete collections of human and mouse retroviral and lentiviral short hairpin RNA (shRNA) libraries from Open Biosystems, and has negotiated with them to distribute clones to UMass researchers (Amherst, Boston, Dartmouth, Lowell and Worcester campuses ONLY) at a reduced price
• Bioinformatics Core: A team of bioinformatics analysts and software engineers dedicated to providing comprehensive bioinformatics and computational infrastructure support for the biomedical research at UMMS.
• Clinical Informatics: Provides support for the conduct, administration, analyses, and dissemination of clinical and translational research from bench to clinic to populations.
• Proteomics and Mass Spectrometry Facility: Offering state-of-the-art proteomic and small molecule mass spectrometric analyses from study and design, sample preparation, protein fractionation, instrumentation, informatics, and data interpretation.
• Small Molecule Screening: Assists researchers in developing high-throughput (HT) screening assays, performs HT screens of chemical libraries to identify new small molecules to probe biological processes of interest.
• Transgenic Animal Modeling Core: To produce genetically-altered mice for UMass Chan researchers. The Core has generated more than 300 different lines of transgenic mice, targeted over 60 genes in mouse ES cells, produced over 120 lines of gene-targeted mice via blastocyst injection, and has cryopreserved over 100 lines of mice.