Dpuiu definitions: Difference between revisions
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* [http://en.wikipedia.org/wiki/Sensitivity_and_specificity Sensitivity and specificity] | |||
Sensitivity=TP/(TP+FN) | |||
Specificity=TN/(TN+FP) | |||
status | |||
outcome + - | |||
+ TP FP | |||
- FN TN | |||
FP: Type I error (P value) | |||
FN: Type II error | |||
try to minimize FP => increase specificity | |||
Sensitive: align as many reads as possible | |||
Specific: avoid misalignments | |||
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* [http://en.wikipedia.org/wiki/Functional_genomics Functional genomics] | * [http://en.wikipedia.org/wiki/Functional_genomics Functional genomics] | ||
* [http://en.wikipedia.org/wiki/Molecular_biology Molecular biology] | * [http://en.wikipedia.org/wiki/Molecular_biology Molecular biology] | ||
* [http://rdp.cme.msu.edu/ Ribosomal Database Project] | * [http://rdp.cme.msu.edu/ Ribosomal Database Project] | ||
* [http://en.wikipedia.org/wiki/IS_element IS elemets] | * [http://en.wikipedia.org/wiki/IS_element IS elemets] | ||
* [http://en.wikipedia.org/wiki/Two-hybrid_screening Yeast two hybrid] , [http://www.google.com/url?sa=t&source=web&ct=res&cd=6&url=http%3A%2F%2Fwww.cs.tau.ac.il%2F~roded%2Fcourses%2Fcsb-08%2FMK2_2.pdf&ei=MU_uSKi0G5y4efirkcwH&usg=AFQjCNHitncQNgToFNcOLXPN1LukNnNs_w&sig2=hVmlT3GKW3fot-cMI3fIZQ Link] | * [http://en.wikipedia.org/wiki/Two-hybrid_screening Yeast two hybrid] , [http://www.google.com/url?sa=t&source=web&ct=res&cd=6&url=http%3A%2F%2Fwww.cs.tau.ac.il%2F~roded%2Fcourses%2Fcsb-08%2FMK2_2.pdf&ei=MU_uSKi0G5y4efirkcwH&usg=AFQjCNHitncQNgToFNcOLXPN1LukNnNs_w&sig2=hVmlT3GKW3fot-cMI3fIZQ Link] | ||
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* [http://en.wikipedia.org/wiki/Purine Purine:AG] 2 rings => bigger | |||
* [http://en.wikipedia.org/wiki/Pyrimidine Pyrimidine:CT] 1 ring | |||
* [http://en.wikipedia.org/wiki/Transition_(genetics) Transition] Purine:Purine or Pyrimidine:Pyrimidine ; 2/3 of the snps | |||
* [http://en.wikipedia.org/wiki/Transversion Transversion] Purine:Pyrimidine or Pyrimidine:Purine ; 1/3 or the snps | |||
---- | |||
* [http://en.wikipedia.org/wiki/Multiple_sequence_alignment MSA] | |||
* [http://en.wikipedia.org/wiki/Phylogenetic_tree Phylogenetic tree] | |||
* [http://www.geneontology.org/GO.doc.shtml GO] | |||
---- | |||
* [http://en.wikipedia.org/wiki/Immunity_(medical) Immunity] | |||
* [http://en.wikipedia.org/wiki/Minimum_inhibitory_concentration MIC] | |||
* [http://en.wikipedia.org/wiki/Horizontal_gene_transfer Horizontal gene transfer] | |||
* [http://en.wikipedia.org/wiki/Gene_therapy Gene therapy] | |||
* [http://en.wikipedia.org/wiki/Wild_type Wild type] typical form of an organism, strain, gene, or characteristic as it occurs in nature; most common phenotype | |||
* [http://en.wikipedia.org/wiki/Gram_negative Gram-negative bacteria] cell walls has an outer membrane; many are pathogenic | |||
----- | |||
* [http://en.wikipedia.org/wiki/Decision_tree Decision_tree] | |||
----- | |||
* [http://en.wikipedia.org/wiki/Machine_learning Machine learning] | |||
* [http://en.wikipedia.org/wiki/Random_forest Random forest] | |||
* [http://en.wikipedia.org/wiki/Neural_network Neural network] | |||
------ | |||
* [http://en.wikipedia.org/wiki/Cross_validation Cross validation] | |||
------ | |||
* [http://en.wikipedia.org/wiki/Genome_project Genome project] | |||
----- | |||
* [http://en.wikipedia.org/wiki/Obligate_intracellular_parasite Obligate intracellular parasite] | |||
----- | |||
* Q20: the number of bases in a read that have a quality value greater than 20; quality value of 20, there is a 1 in 100 chance that the base has been misidentified |
Latest revision as of 14:30, 4 December 2008
Sensitivity=TP/(TP+FN) Specificity=TN/(TN+FP) status outcome + - + TP FP - FN TN FP: Type I error (P value) FN: Type II error try to minimize FP => increase specificity Sensitive: align as many reads as possible Specific: avoid misalignments
- Purine:AG 2 rings => bigger
- Pyrimidine:CT 1 ring
- Transition Purine:Purine or Pyrimidine:Pyrimidine ; 2/3 of the snps
- Transversion Purine:Pyrimidine or Pyrimidine:Purine ; 1/3 or the snps
- Immunity
- MIC
- Horizontal gene transfer
- Gene therapy
- Wild type typical form of an organism, strain, gene, or characteristic as it occurs in nature; most common phenotype
- Gram-negative bacteria cell walls has an outer membrane; many are pathogenic
- Q20: the number of bases in a read that have a quality value greater than 20; quality value of 20, there is a 1 in 100 chance that the base has been misidentified