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://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]
----
* [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










  • 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