University of Rhode Island
- Department of Cell and Molecular Biology
- CMB Bioinformatics Web Resources
- College of the Environment and Life Sciences
- RI EPSCoR
- INBRE Centralized Research Core Facility
- Center for Genomics and Proteomics: This core includes a full complement of proteomics and functional genomics research equipment, capabilities for the production of transgenic and knockout mice, and extensive bioimaging infrastructure. The CGP features Next Generation Sequencing utilizing an Illumina HiSeq 2500 that employs dual flow cells running simultaneously independent of the run type. This instrument can generate up to 2 x 100 bp single and paired-end reads routinely achieving 150-200 million reads per lane and 300 GB of data per flow cell.
- Center of Computation & Visualization: The Brown CCV develops and manages high-performance computing, data storage, and visualization resources, provides physical and virtual server hosting, and offers high-performance backup and archival services for the research community. The CCV also maintains a one-petabyte Tivoli TSM backup/archive server for research data. RI-EPSCoR investigators interested in using the resources of the CCV must apply for access.
National Institutes of Health
- The National Center for Biotechnology Information maintains public sequence databases, genome assemblies, online books, software, and more.
- Chromas Lite by Technelysium Pty Ltd is shareware software for searching, manipulating and exporting sequences into documents or presentations. This software supports the SCF format chromatogram files. For Windows PC only.
- CodonCode offers programs for for sequence assembly, contig editing, and mutation detection for Windows and Mac OS X. Supports base calling with Phred, end clipping, vector trimming, assemble by name, alignment to reference sequences, aligning contigs, analysis of heterozygous insertions and deletions, and much more. The demo version of CodonCode Aligner is a fully functional trace viewer and editor.
- FinchTV by Geospiza is a free trace viewer for DNA sequences in ab1 and scf file formats on Linux, MacOS X, Windows, and Solaris platforms. This chromatogram viewer can display an entire trace in a scalable multi-pane view and also has raw data views, BLAST searching and the ability to reverse complement sequences and traces
- 4Peaks is a free program that helps molecular biologists to visualize and edit their DNA sequence files. 4Peaks can read and write most common trace file formats, and allows direct access to both sequence and translation. It offers the ability to analyze, edit and correct your sequence data. MacOS only.
- Agilent Technologies offers microfluidics-based instruments for sizing, quantification and quality control of DNA, RNA, proteins and cells. The 2100 Bioanalyzer has a broad range of pre-validated analysis kits combined with an easy-to-use benchtop system. Agilent is also the manufacturer of the Mx3005P qPCR system used for gene expression analysis, microarray data validation, SNP genotyping, pathogen detection, DNA methylation analysis, and chromatin immuno-precipitation studies. For an excellent reference, be sure to download their “QPCR – Methods and Applications Guide”.
- Life Technologies / Applied Biosystems is the manufacturer of our 3130xl and 3500xl genetic analyzers. Some very useful free software are: Sequence Scanner (sequencing analysis and viewing program) and Peak Scanner (fragment analysis software).
- Illumina is the manufacturer of our next generation sequencer, the MiSeq. This site contains workflows, reagent kits, tutorials, and applications.
- Roche Applied Science has a wealth of information on the LC480 qPCR system as well as literature and references. A comprehensive list of reagents is also available including the Universal Probe Library system for gene expression studies.