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Genetic Analysis: GWAS Genetic Variation Linkage Analysis Gene Expression
Sequence Analysis: Assembly Annotation Alignment RNAi RNA-seq Primer Design Next Generation Tools Phylogenetic Analysis Gene Structure Viral
The Broad Integrative Genomics Portal allows the sharing (both private and public) of annotated and integrated genomic datasets. Funded by the Starr consortium, the portal provides both data analyses and visualizations.
The Integrative Genomics Viewer (IGV) is a visualization tool to simultaneously integrate and analyze multiple types of genomic data.
InVEx (Introns Vs Exons) is a permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations. The method was developed for use in cancer genomics studies, with particular relevance to high mutation rate cancers. Mutations are permuted on a per-patient, per-trinucleotide-context basis across the exons, introns and UTRs of a gene, generating a null model of the distribution of mutations to which the observed distribution can be compared to determine statistical significance. Significant genes are of interest, as their somatic mutation is likely to be important in the formation of the cancer being studied. The method can operate on whole exome as well as whole genome sequencing data.
Kinannote identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. If the user inputs a complete proteome, additional modules are available to evaluate the completeness of the kinome and place it in context with reference kinomes.
LocusView is a program for generating images of chromosomal regions annotated with genomic features, experimental data, and analysis results.
MAGENTA is a program that tests whether predefined biological processes or gene sets are enriched for genes associated with a complex disease or trait.
MapMaker is a package containing a program for genetic linkage analysis and a program for mapping genes underlying complex traits.
MEDEA is a suite of Adobe® Flash® based comparative genomic visualization tools including a Circular Genome Viewer, parallel Genome Map, Synteny Map, and Dot Plot.
The Multiple Myeloma Genomics Portal (MMGP) provides access to and analysis of the MMGP portal data sets. These include the MMRC-funded reference collection of paired aCGH and gene expression data as well as several additional public multiple myeloma datasets.
The NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST formatted sequences.