Bioinformatics Core

Explosive growth in powerful bioinformatics tools and continued refinements in well-annotated databases have accelerated the acquisition of new knowledge about human genes and proteins that provide the basis for personalized, predictive, preventive and participatory medicine. This revolution in bioinformatics is expected to result in significant improvements in human health and prevention of disease.

Objective

Enhance the infrastructure for the Bioinformatics Core, in support of hypothesis-driven research projects that seek to gain new knowledge about emerging infectious diseases.

Specific Aim 1

Provide optimized support and consultation services in bioinformatics. The Bioinformatics Core will be directly involved in implementation of the COBRE Research Projects by providing individualized consulting services to optimize the use of bioinformatics tools by COBRE Investigators and other researchers in the state of Hawaii. A fully functional infrastructure with bioinformatics software will be made available to the COBRE Investigators, as well as others researchers in the State of Hawaii.

Specific Aim 2

Develop novel bioinformatics tools and innovative methods. The COBRE Bioinformatics Core will actively collaborate with COBRE and INBRE Investigators and other bioinformatics experts in the State of Hawaii. This network of experts will foster the development of novel methodologies and tools that will enrich the bioinformatics tools made available to the research community.

Specific Aim 3

Develop and implement an education and training program in bioinformatics. The COBRE Bioinformatics Core will collaborate in the development of a comprehensive training program involving a workshops series on bioinformatics and biomedical informatics featuring high-profile speakers. The Core Director and Associate Directors will continue to refine and expand the bioinformatics curricula within the Department of Information and Computer Sciences and the John A. Burns School of Medicine.

Please contact Mahdi Belcaid with any questions regarding Bioinformatics Services mahdi[at]hawaii.edu

Citations in Publications

Use of this core facility should be acknowledged in publications, abstracts, posters and oral presentations. The suggested verbiage is:


“Some of the services for this research were provided by the Bioinformatics Core, which is supported in part by grant P30GM114737 from the Centers of Biomedical Research Excellence (COBRE) program of the National Institute of General Medical Sciences, a component of the National Institutes of Health.”

Analysis Services

• Data quality assessment
• Vector, quality and adapter trimming
• Bacterial (small) draft genome assembly (454 or Iillumina data)
• Small metagenome analaysis (diversity of less than 10k species)
• Large scale sequence alignments (depending on the library size) against reference:
• Rna-Seq analysis

Software Licenses

• JMP 10.0, 9.0, 8.0 & 7.0
  More details about the software: JMP
  Downloads:

  • JMP 10 Mac
  • JMP 10 Windows

• VectorNTI 9.1
  More details about the software: Vector NTI
  Downloads:

  • VNTI Suite for OSX
  • VectorNTI Advance 9.1

• CLC Genomics Workbench
  More details about the software: CLC

• Lasergene DNASTAR
  More details about the software: DNASTAR

• Sequencher 4.10.
  More details about the software: Sequencher

Tools developed by the COBRE Pacific Center for Emerging Infectious Diseases Research and INBRE II Hawaii Bioinformatics core team

1- fragAnchor: GPI-Anchored Protein Prediction Tandem System. FragAnchor is based on the tandem use of a Neural Network predictor and a Hidden Markov Model predictor. The Neural Network is used to select the potential GPI-anchored sequences and the Hidden Markov Model classifies the selected sequences according to four different levels of precision (highly probable, probable, weakly probable, potential false positive). The Hidden Markov Model proposes also up to three possible locations for the anchor/cleavage site.


fragAnchor webserver


2- GPI-DB: a GPI-anchor prediction database for fragAnchor. This database contains all the GPI-anchored proteins predicted by fragAnchor, GPI-SOM and predGPI from the proteomes available in the intergr8 database. The predictions are classified following a qualitative scoring (ranking from highly probable to potential false positive). Each prediction gives a maximum of 3 possible structures of the GPI-anchor signal.


GPI-DB database


3- BiL Biohadoop: A graphical user interface, or alternatively a command line tool to run bioinformatic jobs on a compute cluster. This tool presently allows for parallel execution of the following tools: Blast, Bowtie, Bwa, Fastq, and Fastx.


Users who need to run BiL Biohadoop should contact: Mahdi Belcaid mahdi [at] hawaii [dot] edu to obtain an account on the cluster and the standalone interface.


BiL Biohadoop command line tutorial: download


BiL Biohadoop standalone interface tutorial: download

4- Integroomer and Integrammer: Integroomer is a web portal to simplify the process of removing adapters and extracting reads from sequencing data. Integrammer on the other hand, is as web portal that provides basic statistical information on reads extracted by Integroomer.


Intergroomer/Intergrammer

Workshop Series

Draft schedule of the University of Hawaii Bioinformatics and Biomedical Informatics (UHBBI) workshops series (UHBBI): UHBBI workshops

Director:

Guylaine Poisson
Email: guylaine[at]hawaii.edu

Core Supervisor:

Mahdi Belcaid
Phone: 808-956-6049
Email: mahdi[at]hawaii.edu