RNA Web Tools

All UMMS Core Facilities

UMMS Highlighted Core Facilities

• 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
  
  
• UMMS RNAi Core Facility
  UMMS 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 the UMASS Medical School Community. 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.

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.

Data Bases

• Comprehensive Transposon Database
  Public research domain on genetic information (DNA sequence data), as well as dissemination of databases and computer software.
  
  
• European Bioinformatics Institute
  Rfam RNA database and web resource.
  
  
• Gene Expression Omnibus (GEO) 
  Public functional genomics data repository supporting MIAME-compliant data submissions.
  
  
• The mRNA Decay Resource
  Sharing of information, know-how, and wisdom among researchers who study mRNA decay.
  
  
• PDB Protein Databank
  PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.
  
  
• RNA Modification Database
  A comprehensive listing of post-transcriptionally modified nuceosides form RNA.
  
  
• 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.

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 tagets

Model Organisms

• Flybase
  Database of Drosophila and genes and genomes.
  
  
• Bloomington Drosphila 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.

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.

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.

Suppliers

• Dharmacon
  RNAi products and technologies: siRNA, microRNA, shRNA, qPCR assays, RNAi controls, transfections, customs synthesis, ancillary reagents, siDesign center.
  
  
• Genewiz
  DNA sequencing service. Drop box in AS4-2016.
  
  
• IDT
  Oligo design and analysis tools, tutorials
  
  
• Invitrogen
  Molecular and cell biology essentials
  
  
• QIAGEN
  Sample and Assay Technologies for all RNA investigative endeavors focusing on individual targets, pathway- or disease-focused panels, and whole transcriptome profiles.
  
  
• Sigma Proligo
  A dedicated specialist in nucleic acid chemistry