GeneSieve

A Probe Selection Tool for cDNA Microarrays

  Result Analysis  

Analysis


The output from genesieve and the statistics obtained during the various stages of the process of addition of an organism to the Genesieve database can be interpreted in a number of ways to derive interesting and useful qualitative information about the data. This information has been specifically categorized into the following:

  • Clustering using PHRAP This includes information like the total number of ESTs, Contigs and Singletons in the organism.

  • Protein Homology This includes a comparison of the contigs of the organism to the proteins found in Arabidopsis thaliana. The results include an average protein coverage by contigs, the number of ESTs showing similarity to Arabidopsis proteins, all hits of Arabidopsis proteins in the organism and the number of contigs and ESTs which play a role there.

  • Annotation Analysis Here, the proteins in the organism showing homology to the Arbidopsis proteins are categorized into Putative, Unknown, Expressed, Hypothetical and Useful proteins and the number in each category is calculated.

  • Contigs covering 3'/5' ends of Arabidopsis proteins As the subtitle suggests, here a calculation of the number of contigs in each of the following categories is done: contigs covering 5' end, contigs covering 3' end, contigs in the 5' end proximity < 10 amino acids and contigs in the 3' end proximity < 10 amino acids

  • Comparison of Various Selection Methods In this section, ESTs are selected by a variety of factors like maximum length, 5' proximity, 3' proximity, maximum Protein Homology, minimum Cross Hybridization Score, maximum Relative Length, maximum Quality and maximum Quality with cross hybridization score <= 0.5; and the average protein homology score, cross hybridization score, relative length, quality in each selection are computed.


  • Currently, Quality Analysis and related data are available for the following organisms:
  • Pine
  • Potato
  • Tomato
  • Barley
  • Maize
  • Log in to view data for all the above organisms.

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