Download Genome Data

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  Sequencing Institute and Genome
Assembly- by genome sequencing project D5_BGI D5_JGI A2_BGI AD1_BGI AD1_NBI AD2_HAU
FASTA Files            
     * Chromosomes + Scaffolds 13 + 4434 13 + 1020 13 + 75,581 26 + 9128 26 + 288,273 26 + 29,751
     * Chromosomes + Scaffolds with repeats masked by N's sequences   13 + 1020        
     * Chromosomes + Scaffolds with repeats masked by lower case   13 + 1020        
     * Chromosomes only 13 13 13 26 26 26
     * Scaffolds only 4434 1020 75,581 9,128 288,273 29,751
     * Other anchored sequences           17,434
GFF3 | EXCEL | TXT  Files            
     * Chromosomes + Scaffolds 13 + 4434 13 + 1020 13 + 75,581 26 + 9128    
     *  Assembly GAPs   8879        
Annotation - by genome sequencing project D5_BGI D5_JGI A2_BGI AD1_BGI AD1_NBI AD2_HAU
FASTA Files            
    * Predicted coding sequences 40,976 77,267 40,134 76,943 70,478 109,918  
    * Predicted protein sequences 40,976 77,267 40,134 76,943 70,478 109,918
    * Predicted gene sequences   37,505       80,876
GFF3 | EXCEL | TXT  Files            
    * Genes            
          - Predicted gene alignments FTP FTP FTP FTP FTP FTP
          - Predicted gene with exon alignments   FTP        
    * Structural            
          - De novo repeats alignments FTP          
          - Repeats identified using RepeatMasker alignments FTP FTP        
          - Repeats identified using RepeatMasker ProteinMask alignments FTP          
          - Repeats identified using 'trf' alignments FTP          
          - miRNA alignments FTP          
          - Ribosomal RNA alignments FTP          
          - snRNA alignments FTP          
          - tRNA alignments FTP          
    * Functional            
          - Functional assignments         FTP FTP
          - GO assignments       FTP    
          - InterPro assignments       FTP    
          - KEGG assignments       FTP    
          - SwissProt assignments       FTP    
          - TrEMBL assignments       FTP    
    * Transcripts            
          - PASA mapped Phytozome ESTs*   FTP        
Annotation - by CottonGen or cotton research group(s) D5_BGI D5_JGI A2_BGI AD1_BGI AD1_NBI AD2_HAU
GFF3 | EXCEL | TXT  files            
    * Functional            
          - Interpro Analysis       FTP FTP FTP
          - GO assignments from InterProScan FTP FTP FTP FTP FTP FTP
          - IPR assignments from InterProScan FTP FTP FTP FTP FTP FTP
          - Genes in KEGG Pathways FTP FTP FTP FTP FTP FTP
          - Genes mapped to KEGG orthologs FTP FTP FTP FTP FTP FTP
          - KEGG hier file   FTP FTP      
          - KEGG image maps   FTP FTP      
    * GenSAS Analysis            
          - Repeat Masker   FTP FTP FTP FTP FTP
          - Repeat Masked Sequence   FTP FTP     FTP
          - Repeat Modeler   FTP FTP FTP FTP FTP
          - SSR   FTP FTP FTP FTP FTP
          - tRNAscan   FTP FTP FTP FTP FTP
    * Marker Alignments            
          - CottonGen RFLP markers FTP FTP FTP FTP FTP FTP
          - CottonGen SSR markers FTP FTP FTP FTP FTP FTP
          - CottonGen SNP markers FTP FTP FTP FTP FTP FTP
          - CottonGen InDel markers FTP FTP FTP FTP FTP FTP
    * SNP Sequence Alignments            
          - NCBI dbSNP-cotton (built on 2011-07-21)   FTP   FTP FTP FTP
          - Udall Lab's A/D (diploid) SNPs   FTP        
          - Udall' Lab's At/Dt (tetraploid) SNPs   FTP        
    * Protein Alignments            
          - Arabidopsis thaliana TAIR10   FTP FTP FTP FTP FTP
          - Glycine max v1.0 (annotation version)     FTP FTP FTP FTP
          - Oryza sativa MSU v7.0    FTP FTP FTP FTP FTP
          - Poplar trichocarpa (assembly version)            FTP FTP FTP
          - Theobroma cacao v1.1   FTP FTP FTP FTP FTP
          - Vitis vinifera     FTP FTP FTP FTP
          - NCBI nr-cotton (download date)      FTP (08/14) FTP (07/15) FTP (07/15) FTP (02/16)
          - Uniprot swissprot-cotton (download date)       FTP (07/15) FTP (07/15)  
          - Uniprot trembl-cotton (download date)     FTP (08/14) sptr FTP (07/15) FTP (07/15) FTP (02/16) sptr
          - NCBI nr-all (download date)            
          - Uniprot swissprot-all  (download date)            
          - Uniprot trembl-all (download date)            
    * Protein Homologies            
          - Arabidopsis thaliana TAIR10 FTP FTP FTP FTP FTP FTP
          - Glycine max v1.0 (annotation version)     FTP FTP (a2) FTP (a2) FTP
          - Oryza sativa MSU v7.0 FTP FTP FTP FTP FTP FTP
          - Poplar trichocarpa (assembly version)   FTP FTP (v2)   FTP (v3)  FTP (v3)   FTP 
          - Theobroma cacao v1.1 FTP FTP (v0.9) FTP FTP  FTP FTP
          - Vitis vinifera (assembly version) FTP   FTP FTP (v12) FTP (v12) FTP
          - NCBI nr-cotton (download date)           FTP (02/16) 
          - Uniprot swissprot-cotton (download date)            
          - Uniprot trembl-cotton (download date)           FTP (02/16) sptr
          - NCBI nr-all (download date) FTP (10/12) FTP FTP      
          - Uniprot swissprot-all (download date) FTP (10/12) FTP FTP      
          - Uniprot trembl-all (download date) FTP (10/12) FTP FTP      
    * Unigene & Transcript Alignments             
          - CottonGen unigene v1.0 FTP FTP FTP FTP FTP FTP
          - J. Udall 2012 Unigene contigs FTP FTP FTP FTP FTP FTP
          - J. Udall 2012 Unigene CDS     FTP   FTP FTP
          - PlantGDB Gossypium unigenes FTP FTP FTP FTP FTP FTP
          - PlantGDB G. arboreum v157a unigenes FTP FTP FTP FTP FTP FTP
          - PlantGDB G. barbadense v183a unigenes FTP FTP FTP FTP FTP FTP
          - PlantGDB G. hirsutum v165a unigenes FTP FTP FTP FTP FTP FTP
          - PlantGDB G. raimondii v157a unigenes FTP FTP FTP FTP FTP FTP
          - TIGR/DFCI Cotton Gene Index v11 unigenes     FTP FTP FTP FTP
          - NCBI Gossypium unigenes     FTP FTP FTP FTP
          - NCBI G. hirsutum unigenes     FTP FTP FTP FTP
          - NCBI G. raimondii unigenes     FTP FTP FTP FTP
          - NCBI Gossypium ESTs (download date) FTP (10/12) FTP (10/12) FTP (08/14) FTP (07/15) FTP (07/15) FTP (02/16)
          - NCBI G. arboreum ESTs (download date) FTP (10/12) FTP (10/12) FTP (08/14) FTP (07/15) FTP (07/15) FTP (02/16)
          - NCBI G. barbadense ESTs (download date) FTP (10/12) FTP (10/12) FTP (08/14) FTP (07/15) FTP (07/15) FTP (02/16)
          - NCBI G. herbaceum ESTs (download date) FTP (10/12) FTP (10/12) FTP (08/14) FTP (07/15) FTP (07/15) FTP (02/16)
          - NCBI G. hirsutum ESTs (download date) FTP (10/12) FTP (10/12) FTP (08/14) FTP (07/15) FTP (07/15) FTP (02/16)
          - NCBI G. raimondii ESTs (download date) FTP (10/12) FTP (10/12) FTP (08/14) FTP (07/15) FTP (07/15) FTP (02/16)
          - NCBI Gossypium mRNAs (download date) FTP (10/12) FTP (10/12)