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Bioinformatics Core

Software

Software

Internal Bioinformatics Resources

  • Microarray Analysis
    • HSPH is installing a web server for do-it-yourself microarray analysis. Expert help will still be available. The server should be up and functioning by the first quarter of 2008. Until then, please feel free to contact the Bioinformatics Core Helpdesk for expert hands-on help with your analysis needs. 
  • Systems Biology/Analysis Resources
    • GeneGO's Metacore (license only). Systems/pathway/functional analysis of gene lists. Takes many different types of identifiers for human, mouse, and rat data, performs analysis for pathways, networks of function, provides statistics for enrichment. Returns genes, likely transcription factors linked to gene lists, enrichment over hundreds of annotated pathways, diseases, biological processes, more. Underlying database has over 2,000,000 interactions, most generated from expert curation. HSPH licenses one seat in 2007/8: if you wish a password and tutorial to use this software, contact the Bioinformatics Core Helpdesk.

External Resources 

  • Sequence manipulation, vector design, alignment, other.
    • BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP.  Need a Windows virtual machine to run on Mac (but works well in emulators). An intuitive multiple document interface with convenient features makes alignment and manipulation  of sequences relatively easy on your desktop computer. 
    • pDRAW  Useful Windows/PC software for vector design, figure generation, "virtual gels", general DNA analysis.
    • Artemis   Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, and is available for UNIX, GNU/Linux, BSD, Macintosh and MS Windows systems. 
  • General statistics and data analysis
    • R - (R statistical language)
    • Bioconductor - ( An open source and open development software project for the analysis and comprehension of genomic data, based on R language )
    • UBIC2
    • SAS Genetics on HSPH Server - (More information: PDF1, PDF2)
  • Database and data integration
    • Bio.net - (The Bio.Net project uses .Net technologies to pursue scalable communication, combination, and coordination among various types of biology databases )
    • BIND - The Biomolecular Interaction Network - ( The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature. )
    • GeneNotes - (Integrate various data bases and literature information of a specific list of genes, WebVideo tutorial, Yahoo! GeneNotes User Group)
    • GeneCards - (GeneCards® is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others.)
    • GeneNote - (GeneNote is a full-genome database of expression in healthy human tissues. We present the full transcriptome for both known and novel genes.)
    • GeneAnnot - (annotation of Affy probe sets, by Weizmann Ins.)
    • GeneLoc - (Formerly known as The Unified Database for Human Genome Mapping (UDB))
    • GeneTide - (GeneTide is an automated system for human transcripts (mRNA & ESTs) annotation and elucidation of de-novo genes.)
  • Motif Finding
    • Bioprospector - ( Finding regulatory sequence motifs by Gibbs sampling strategy )
    • MDscan - (Combines the advantages of word enumeration and position-specific weight matrix updating, and incorporates the ChIP enrichment information to accelerate the search and enhance success rate )
    • MotifBooster - (A boosting approach for modeling TF-DNA binding )
    • MotifRegressor - (Use expression data to help motif finding. )
    • CompareProspector
    • SeqVista