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Bioinformatics

DNA

Bioinformatics resources at CCR currently provide users with access to enterprise level genomics packages and software for DNA and protein sequence analysis, database search, gene expression analysis, biological pathway analysis, statistical computing, and inferring phylogenies. In addition to access to software packages, CCR staff, who have extensive expertise in bioinformatics, provide researchers with detailed data analysis support as well as custom software design.

Access to all applications requires a login account. The web portals have separate logins. If you are a researcher and would like to have an account with us, please apply for an account.

Tools Developed & Installed at CCR

miRdSNP miRdSNP is a custom database that allow the user to explore disease-associated SNPs (dSNPs) on the 3'UTRs of human genes and their special relationship with miRNA target sites.  miRdSNP includes data from computationally predicted microRNA target sites and manually curated dSNPs.  The advanced web interface allows users to perform proximity searches between miRNA target sites and dSNPs by gene name, miRbase ID, target prediction algorithm, disease, and any nucleotide distance between dSNPs and miRNA target sites.    Developed at CCR.  More Information
REDfly Portal REDfly  is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs). Despite more than 20 years of experimental determination of these elements, the data have never been collected into a single searchable database.  REDfly has an active international user base and averages between 200-250 unique users per month, not including access to the data through other avenues including FlyMine, FlyTF, DroID, and FlyBase.  Developed at CCR.
xTuition A tool for exploring information on the process of macromolecule crystallization for use in drug discovery. By utilizing chemical knowledge and laboratory data collected from over 20M crystallization experiments using more than 12,500 biological macromolecules, the rate for successful crystallization can be improved.  xTuition seeks to utilize knowledge of the chemical properties of the salts, PEGS, and commercial crystallization screens used during crystallization to suggest improvements to the process.  This is being developed in collaboration with HWI.
SNP Phylogeny Mapping

A pattern discovery tool that takes as input a phylogenetic tree and a table of SNP data and outputs SNP solutions for every branch in the phylogenetic tree. This tool was originally developed for the DHS for use in a pathogen detection system.  Contact CCR Help for more information.

 

Biomarker Analysis Pipeline This pipeline consists of a suite of tools toward the statistical analysis of MALDI-TOF spectra, accessible via web interface.
RNA Drug Binding Prediction Algorithm A genetic algorithm that uses a database of drug-RNA binding data to accurately predict binding constants (Kd’s) of unknown RNA loop structures. This technique can greatly speed up the drug discovery phase and has the potential to speed up the process of finding cures for RNA-mediated diseases such as Myotonic Muscular Dystrophy and Huntington's disease.
NGS Portal A flexible and easy-to-use interface that could serve as a cohesive force to provide a full picture of the possibilities of NGS to the experimentalist. Abilities to analyze, annotate, visualize, and compare different results all exist but are incomplete, incompatible, disparate, highly specialized, and do not integrate well with existing custom in-house pipelines. We are developing a NGS portal which allows users to browse reduced NGS results in the context of the reference genome, initiate custom analyses, and view those results alongside other results while displaying relevant annotations retrieved from databases.   Under development at CCR.

Other Tools Installed on CCR Supported Machines

Next Generation Sequence Analysis

Contact CCR Help for more information.

Ingenuity IPA Software Ingenuity systems IPA software is optimal for pathway analysis, microRNA, NGS, RNA-Seq, microarray, biomarker, gene expression and toxicity scientific research.  Limited licenses available to CCR staff.  Please contact Dr. Zihua Hu for more information.
Proteomics analysis

Installed and maintained by CCR for several proteomics labs affiliated with UB.  Please contact CCR Help for more information.

BLAT A DNA alignment tool similar to BLAST, which uses an index of the genome in machine memory.  Requires a CCR account to access see More Information for details.
Galaxy Galaxy is an open source, web-based platform for data intensive biomedical research.  CCR maintains it's own Galaxy installation and will install tools by request.

Tools Installed on CCR Linux Cluster

Next Generation Sequence Analysis

Contact CCR Help for more information.

Proteomics analysis Myrimatch MS-MS Database Search
Rosetta Rosetta Commons is a protein sequence analysis suite.  More Information
CS-Rosetta CS-Rosetta is a suite for chemical shifts based protein structure prediction using ROSETTA.  More Information
BLAST & MPI-BLAST

BLAST (Basic Local Alignment Search Tool) finds regions of local similarity between sequences.  More information

MPI-BLAST is a parallel version of NCBI BLAST.  More Information

R and Bioconductor

R is an integrated suite for statistical computing and graphics. More Information

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. 

EIGENSOFT EIGENSOFT is a software suite for population genetics methods and the EIGENSTRAT stratification method.  More information
EMBOSS EMBOSS is the European Molecular Biology Open Software Suite.  More Information
MATLAB MATLAB integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation. More Information
HMMER & MPI-HMMER

HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.  More Information

MPI-HMMER is a multiple-level optimization of the original HMMER 2.3.2 code that consists of two distinct optimizations: a portably tuned P7Viterbi function as well as an MPI implementation.  More Information

MrBayes MrBayes is a parallel program for the Bayesian estimation of phylogeny.  More Information

Support & Services

CCR provides extensive scientific and programming support to the Bioinformatics community.

Scientific Analysis
Bioinformatics and computational biology support include the development of customized tools and approaches to support faculty led research and advanced data analysis and mining for research projects. Contact Dr. Zihua Hu for more information.

Database Design
CCR provides advanced database support including customized database schema design, import and normalization of data, query optimization and data warehousing. Contact Steve Gallo for more information.

Scientific Programming
CCR's scientific programming staff has expertise in the a number of programming languages including C, C++, Java, PHP, Perl, and Fortran, among others. This group provides custom code, interface and web portal solutions to facilitate faculty led research. Contact Steve Gallo for more information.

Check it out!

CCR has developed and submitted tools to the bioinformatics developer community!  Find us on GitHub