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Table 3 Annotation statistics for ESTIMA:Songbird Build 3

From: The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution

  Build 3 Percent total 20 K array subset Percent of array Percent of Build 3 category
Unique sequences after assembly 31658 100% 17214 100% 54%
A) ALL HITS BY DATABASE      
   Gga Genome 21601 68% 12396 72% 57%
   Chicken_TC 20208 64% 11715 68% 58%
   Gga Unigene 17980 57% 10490 61% 58%
   NCBI_Chicken_RNA 15904 50% 9110 53% 57%
   Ensembl_Chicken_cdna_all 14609 46% 8348 48% 57%
   Ensembl_Chicken_cdna_abinitio 13223 42% 7588 44% 57%
   Chicken IPI 13219 42% 7898 46% 60%
   Hs Unigene 12373 39% 7224 42% 58%
   NCBI_Chicken_protein 7776 25% 4517 26% 58%
Hits against any database 24466 77% 13803 80% 56%
B) Hierarchy of CUSTOM ANNOTATION      
   1 Use IPI-annotation* 13219 42% 7553 44% 57%
   2 in GGA_Unigene but not IPI 5614 18% 3364 20% 60%
   3 in HS but not IPI or GGA_unigene 265 1% 104 1% 39%
Total number of "custom annotations" 19098 60% 11021 64% 58%
   4 additional "conserved in chicken" 5368 17% 2784 16% 52%
Hits against any database 24466 77% 13805 80% 56%
   5 remainder = "TGU-specific" (no hits) 7192 23% 3409 20% 47%
  31658 100% 17214 100% 54%
*C) IPI Annotations      
   Number of sequences with IPI identifiers 13219   7898 (Unigene used for 345)
   Number of unique IPI identifiers 8127   6035   
All identifiers in IPI release 3.26 25500   25500   
   Fraction of total IPI identifiers 32%   24%