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software [2014/03/31 14:55]
dmjordan
software [2016/11/18 16:06]
schun
Line 3: Line 3:
 We develop and maintain a variety of software and web services. We develop and maintain a variety of software and web services.
  
-===Tools for Assessment of SNPs=== +===Tools for Assessment of Variants=== 
-* [[http://​genetics.bwh.harvard.edu/​pph2|PolyPhen-2]] is a tool for predicting the effect of an amino acid substitution on protein structure and function, based on comparative genomics and experimentally determined protein structures. It is available as a web service, and can also be downloaded as a standalone application. +  * [[http://​genetics.bwh.harvard.edu/​pph2|PolyPhen-2]] is a tool for predicting the effect of an amino acid substitution on protein structure and function, based on comparative genomics and experimentally determined protein structures. It is available as a web service, and can also be downloaded as a standalone application. 
-* [[http://​genetics.bwh.harvard.edu/​snptrack|SNPtrack]] is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service. +  * [[http://​genetics.bwh.harvard.edu/​snptrack|SNPtrack]] is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service. 
-* [[http://​genetics.bwh.harvard.edu/​scone/​|SCONE]] is a tool for predicting the effect of noncoding variation on regulatory sequences based on evolutionary conservation. It is available for download as a standalone application.+  * [[http://​genetics.bwh.harvard.edu/​scone/​|SCONE]] is a tool for predicting the effect of noncoding variation on regulatory sequences based on evolutionary conservation. It is available for download as a standalone application
 +  * [[http://​genetics.bwh.harvard.edu/​pines/​|PINES]] (Phenotype-Informed Noncoding Element Scoring) evaluates the functional impact of noncoding variants by integrating diverse epigenetic annotations,​ utilizing genomic annotations most relevant to phenotypes of interest.
  
 ===Tools for Mass Spectrometry and Proteomics=== ===Tools for Mass Spectrometry and Proteomics===
-* [[http://​genetics.bwh.harvard.edu/​cgi-bin/​msfilter/​eagleeye.cgi|EagleEye]] is a tool for filtering noise and background proteins from LC-MS/MS spectra. It is available as a web service. +  ​* [[http://​genetics.bwh.harvard.edu/​cgi-bin/​msfilter/​eagleeye.cgi|EagleEye]] is a tool for filtering noise and background proteins from LC-MS/MS spectra. It is available as a web service. 
-* [[http://​genetics.bwh.harvard.edu/​msblast|MS-BLAST]] is a tool for searching protein sequences identified with tandem mass spectrometry against databases of protein sequences. It is available as a web service.+  * [[http://​genetics.bwh.harvard.edu/​msblast|MS-BLAST]] is a tool for searching protein sequences identified with tandem mass spectrometry against databases of protein sequences. It is available as a web service. 
 + 
 +===Tools for Statistical Genetics=== 
 +  * JLIM is a tool to test for shared genetic effect between two genetic association data, for example, a disease GWAS study and gene expression QTL (eQTL) study.