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Short description:
Please summarise the application in a few sentences. Avoid links here. Program to detect copy number variation in inbred mouse strains
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Copy number estimation,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
Wellcome Trust Sanger Institute,
We have developed an algorithm to detect copy number variants (CNVs) in homozygous organisms, such as inbred laboratory strains of mice, from short read sequence data. Our novel approach exploits the fact that inbred mice are homozygous at virtually every position in the genome to detect CNVs using a hidden Markov model (HMM). This HMM uses both the density of sequence reads mapped to the genome, and the rate of apparent heterozygous single nucleotide polymorphisms (SNP), to determine genomic copy number.
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