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What is it?

MIT's Broad Institute maintains an extensive list of original and high quality software programs for analyzing sequence, expression, and statistical genetics data.

What's available?

Genome Sequence

• Arachne: tool for assembling genome sequences from whole genome shotgun reads, mostly in forward-reverse pairs obtained by sequencing clone ends.
• Argo: Genome Browser tool for visualizing and manually annotating whole genomes.

Genetic Variation

• EIGENSTRAT: detects and corrects for population stratification in genome-wide association studies using principal components analysis.
• Haploview: facilitates the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.
• Locusview: a program for generating images of chromosomal regions annotated with genomic features, experimental data and analysis results.
• PLINK: a comprehensive toolset for statistical analysis in whole-genome association studies
• Sweep: allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection.
• Tagger: web server for the selection and evaluation of tag SNPs from genotype data.

Linkage Analysis

• GeneHunter: a tool for rapid extraction of complete multipoint linkage analysis using both parametric and nonparametric approaches.
• MapMaker3: package containing a program for genetic linkage analysis and a program for mapping genes underlying complex traits.

Expression Analysis

• GenePattern: package for the analysis of molecular profiles, e.g., genome-wide microarray expression signatures. It includes a collection of analytic and visualization tools, interfaces for the easy construction of analytic pipelines and integration of new modules without additional programming. Gene Pattern is available for MacOS, Windows, and Linux platforms.
• Gene Set Enrichment Analysis (GSEA): computational method that determines if a given set of genes shows statistically significant differences between two biological states. It is useful for interpreting the results of gene expression studies.
• GeneCruiser: annotation tool that allows users to map genes from genomic databases to Affymetrix probes, find information about Affymetrix probes in genomic databases and find where Affymetrix probes are located in the human genome.
• Connectivity Map: collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of decisive functional connections between drugs, genes, and diseases. This web interface is designed to allow biologists, pharmacologists, chemists and clinical scientists to use our analysis tools, and access the raw data.

Other

• Primer3: tool used to choose primers for PCR reactions.
• RHMapper: web-based Program that allows researchers to map STSs relative to the radiation hybrid map of the human genome.

Source

Lane Librarian

Record created 10/26/2006.