Bioinformatics Services & Software
Please contact us at firstname.lastname@example.org with NGS-related inquiries.
Support for All Major Platforms
The Nevada Center for Bioinformatics is pleased to announce support for Nevada researchers performing Next-Generation Sequencing (NGS) experiments (Life Technologies Ion Torrent, SOLiD, Illumina, and Roche 454 sequencers).
The Center for Bioinformatics offers support for pre-experimental consultation and design, de novo sequence assembly, reference alignment, functional annotation, variant identification, and quantitative RNA-seq pipelines. We encourage researchers to contact us for consultations, including sequencing cost estimates, sound experimental design, and customized analysis. If you are preparing a Next-Generation Sequencing run, but are uncertain which platform is best for your study, the Center can help. We will help you identify suitable platform(s), sequencing strategies (replicates, paired-end, mate-pairs, sample multiplexing), how much sequencing to perform, and the software tools with which to process and analyze the results.
De Novo Assembly
The Center for Bioinformatics can analyze your NGS data to transform millions of sequence reads into meaningful results. We support all the major NGS platforms, including Life Technologies Ion Torrent, SOLiD, Illumina, and Roche 454 sequencers. The Center can perform de novo assembly of genomic and transcript sequences using a variety of software platforms.
The Center also supports applications based upon the alignment of NGS sequences to known references, such as RNA-seq and resequencing. We use standard analytic pipelines (e.g. Bowtie-TopHat-Cufflinks) for RNA-seq experiments to align sequences and identify significant differences in gene expression. Quality control and statistical tests are customized for each experiment. Our resequencing toolkit includes SAMtools and GATK.
The Center for Bioinformatics works closely with university IT to assess and comply with all new HIPAA compliancy regulations for the generation and storage of human genomic data.
estLIMS is an automated EST analysis pipeline and LIMS (Laboratory Information Management System). It tracks Principal Investigators, projects, samples, costs.
As an EST analysis pipeline, estLIMS:
- Processes sequence files;
- Cleanses and clusters raw sequence files using phred, phrap, cross-match, consed;
- Incorporates a custom-cleanse and vector calling;
- Annotates for automatic NCBI submission and FASTA output;
As a Nevada academic researcher, you may use estLIMS from your desktop. Please contact the Center if interested.
The DeCypher Accelerated Biocomputing Solutions is a system for accelerated bioinformatics algorithms, making use of a hardware accelerator card to optimize bioinformatics search and analysis algorithms (e.g. BLAST), and delivers the computational power of at least 75 processor cores.
DeCypher runs all types of BLAST searches. As a Nevada academic researcher, we are pleased to offer you the DeCypher services at no cost. Standard query databases are included and specialized databases can be installed at your desktop with the Center’s support. Contact us to learn more about DeCypher.
The Center provides comprehensive tools for molecular modeling and visualization with licenses for the the following software packages: SYBYL®, Insight II (Accelrys), and Discovery Studio Modeler (Accelrys). These large commercial packages provide an overall modeling environment in which one can use modules to perform diverse calculations ranging from sequence analysis to structure prediction to thermodynamic and kinetic analysis of atomic interactions. The Center supports AMBER, which is currently running on the university research grid SGI Octane2 and Fuel workstations with stereoscopic graphic capabilities designated for molecular modeling Use these from your desktop (or ours), without cost.
The popular GeneSifter™ microarray analysis software provides analysis and storage support for common platforms (Affymetrix, Agilent, Codelink, etc.) as well as for custom arrays. GeneSifter includes analysis options that enable researchers to determine both statistical and biological significance of microarray data in a simple to use Web-based system. GeneSifter is currently available through the Center. Please contact the Bioinformatics department for access to this software. XRAY is a user-friendly add-in for Microsoft Excel. It can be used for general quality control as well as generating gene lists via statistical tests.
Custom SNP data analysis tools are provided for Genome Wide Association Studies to examine possible associations between disease and genotype. Please contact us to arrange custom analysis. The Center for Bioinformatics asks that researchers allow for at least two weeks for the Center to process analysis requests.
The University Research Grid supplies a combined 1.9 TB of RAM and 818 processor cores. A dual Sun Fire X4500 server provides 24 TB of storage. Please contact us for access to this supercomputing power.
The Center maintains several servers with more than 50TB of space for data storage.
The Center is open daily for consulting in a number of bioinformatics areas, including the development of experimental designs, data analysis and mining, programming, streamlining, etc. We also can supply you with access to the university research grid, as well as access to personal computers or workstations, and data storage servers.