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All the common gene models were annotated against the NCBI Non redundant (nr) protein database and Tair 10  protein database using BlastX similarity search on stringent parameters. The common gene models were also searched for their similarity with the NCBI G. hirsutum EST's (assembled). A large number of genes were found novel with respect to G. hirsutum as they didn't have any hits.

For the functional annotation, the common gene models assigned with a Tair locus Id were categorised in different GO categories (cellualar component, molecular function and biological process) using Tair Gene Ontology annotations tool. Gene models with Tair locus id were also search for the KO Ids on KEGG Automatic Annotation Server (KAAS) and subjected to KEGG pathways analysis on the Kyoto Encyclopedia of Genes and Genomes (KEGG) server. For the next level of annotation, blast with NCBI CDD protein database was also performed.

  Annotaions Details of common gene models with different databases  
Annotation details
Database NCBI nr  Tair 10  Cotton ESTs
Total hits 56246 47464 41361
Unique gene models 36745 16296 19270
Functional Annotations 
Tair GO annotation Biological Process 46093
Cellular components 25555
Molecular Function 32924
KEGG Analysis KO id assigned 3248
Pathways identified  87
CDD similarity search Total hits 23819
Pfam domains 9152    
  Functional annotation of the common gene models into different GO categories  
  Details of top 20 pathways identified using KEGG annotations  
Pathways  Gene Count
Metabolic pathways  734
Biosynthesis of secondary metabolites  343
Microbial metabolism in diverse environments  125
Ribosome  111
Spliceosome  93
RNA transport  86
Purine metabolism  81
Oxidative phosphorylation  76
Protein processing in endoplasmic reticulum  73
Pyrimidine metabolism  71
Cell cycle  52
Ubiquitin mediated proteolysis  52
Ribosome biogenesis in eukaryotes  51
mRNA surveillance pathway  46
RNA degradation  44
Plant hormone signal transduction  42
Amino sugar and nucleotide sugar metabolism  36
Nucleotide excision repair  35
Photosynthesis  34
Proteasome  34