Informatics Core Service

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Dana-Farber Bioinformatics core (MBCRR)

Please send comments, complaints, or requests to Matthew Temple

Informatics Core Service: Description of Services

Note: For further information, Email Tom Graf (tom@mbcrr.harvard.edu)

The Informatics Core Service, also known as the MBCRR (Molecular Biology Computer Research Resource) is a critical component for providing research support to Dana-Farber Cancer Institute researchers. It also provides support and receives additional revenue from many of the Boston area teaching hospitals as well as many of the local educational institutions. The facility supports researchers from Boston University, Beth Israel, Brigham & Williams, Children’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, and Harvard School of Public Health. Currently the Informatics Core Service supports about 40 labs inside Dana-Farber Cancer Institute. The Informatics Core Service provides the necessary equipment, software, and personnel to support these researchers as they process raw sequence data from the Molecular Biology Core Facility and other similar facilities.

For information on how to connect to our Unix system, please click on the following link. Secure Shell Access

To search our local specialized databases with BLAST please click on the following link. Search Blast Databases

The Informatics Core Service facility not only provides web-based user accounts and shell-based Unix user accounts on the computer system, but it also provides a comprehensive set of sequence analysis tools. Furthermore, it backs up the software programs it offers with frequent and comprehensive training sessions, ranging from the narrowly mechanical use of these tools, to the more complex issues of when and how best to use these tools. This is invaluable to our local DFCI community because in many labs there is a turnover of postdocs and graduate students every two to four years. These individuals need to be aware of what tools are available to help them in their current research problems, and more importantly, the best tool for the job.

The Informatics Core Service provides a weekly training session which gives an overview of the Genetics Computer Group (GCG) sequence analysis package, as well as how to use other software such as EMBOSS and PHYLIP which complements the tools in this package. Labs that have unique needs are provided with tailor made group training workshops. The Informatics Core Service also provides consulting services in the one-on-one training appointments where a researcher will come with a specific problem not covered by the weekly training workshops and be consulted on how to solve this problem in a hands on manner.

The Informatics Core Service facility supports activites involving new and ongoing user training and support for software accessing public databases such as GenBank, GenPept, Refseq, Refpep, PIR, SwissProt, Prosite, and GenPept Daily. All of these databases are regularly downloaded to our server when new versions are available, and then converted and put into a format for our local database access programs. Researchers with special needs are instructed on how to take their own sequence information and create customized databases in the format required for database searching with local software.

To see a detailed list of the supported software and services on the mbcrr computer systems, click on the following link SOFTWARE

The most commonly supported software is :

BLAST LOCAL Dbs (Basic Local Alignment Search Tool Program) —Scans DNA or Protein sequence against our local databases.

BLAST (Basic Local Alignment Search Tool) —Use Blast Command line interface.

• Keyword Searching —Software to find sequences and MEDLINE documents by query terms.

• DNA translation software-To find open reading frames and predict gene structure from proteins.

• RNA secondary structure prediction software-To predict optimal and suboptimal folding structures.
• Fragment Assembly software-To assemble overlapping fragment sequences.

staden (Sequence analysis package for assembling gels.)

phrap (Shotgun sequence assembly package.)

consed (Consed is a Graphical Tool for Editing Phrap Assemblies.)

phred (Phred reads DNA sequencer trace data and assigns quality values.)

swat (Phrap-swat shotgun sequence assembly package.)

• Mapping software-To analyze sequence for enzyme and restriction sites.
• Primer Selection-To analyze template DNA sequences and choose primer pairs for PCR.

• Protein secondary structure prediction software-To run Chou-Fasman or Garnier-Robson algorithms.
• Protein analysis software-Helical wheel representations, isoelectric points, and molecular weight.
• Hydrophilicity prediction software-According to Kyte-Doolittle or Hopp-Woods algorithms.
• Molecular graphics packages for rendering images such as Raster3D and Molscript.
• R - a language for data analysis and graphics.
• FastLink-a suite of software for doing genetic linkage analysis.
• Tertiary structure prediction tools-To predict possible protein three dimensional structure.
• Gibbs Motif Sampler-For identifying motifs and conserved regions in DNA or protein sequences.
• Multiple Sequence alignment-For protein or DNA alignments and domain searching.(Such as pima, clustalw and mummer
• Evolutionary Analysis-Software such as PAUP and Phylip to perform phylogenetic analysis.
• Gene Prediction such as Glimmer (Gene Locator and Interpolated Markov Modeler).
• More complex pattern searches based on conserved domains to fish out other members.
• Programs to make presentable postscript, or PICT formated publication quality versions of data.