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  • High quality reads used for assembly:


    High quality reads:    FTP


    Assembly data:


    1. Genome sequence:    FTP    HTTP    ReadMe (update 2010-3-25)
    2. Contig locations:    FTP    HTTP

    Gene annotation:


    Gene sets: (Include two homology-based and two de novo gene sets, and a merged reference gene set)

    1. De novo prediction by Augustus software    FTP    HTTP
    2. De novo prediction by Genscan software    FTP    HTTP
    3. Homology based gene set to dog    FTP    HTTP
    4. Homology based gene set to human    FTP    HTTP
    5. The merged reference gene set (merge the above four gene sets)    FTP    HTTP

    Functional annotation for the reference gene set: (Include GO, InterPro, and PANTHER)


    Gene Ontology (GO) annotation for the reference gene set:    FTP    HTTP
    InterPro domain annotation for the reference gene set:    FTP    HTTP
    PANTHER annotation (similar to GO) for the reference gene set: (only served for ftp)    FTP    HTTP

    Non-coding RNA genes: (Include tRNA, rRNA, miRNA, snRNA, combined as a single file)


    Non-coding RNA genes:    FTP


    Regulatory elements:


    1. CpG islands    FTP    HTTP
    2. EP3 predicted promoters:    FTP    HTTP
    3. CpGProD predicted promoters:    FTP    HTTP

    Repeat (include dispersed TEs and tandem repeats)


    1. Protein level identified TEs by RepeatProteinmask software:    FTP    HTTP
    2. RepeatMasker identified TEs using Repbase library:    FTP    HTTP
    3. RepeatMasker identified TEs using a panda-specific library made by RepeatModeler:    FTP    HTTP
    4. Tandem repeats identified by RepeatMasker (include Simple_repeat, Satellite and low_complexity)    FTP    HTTP
    5. Tandem repeats identified by TRF software:    FTP    HTTP

    Whole genome alignments:


    1. Panda versus Dog pairwise alignment    FTP    HTTP
    2. Panda versus Human pairwise alignment    FTP    HTTP
    3. Conserved elements identified on 5-way multiple alignments by PhastCons software:    FTP    HTTP

    Heterozygosity of the diploid genome: (Include SNP, Indel, and SV)


    1. SNP:    FTP    HTTP
    2. Small Indel (1-6 bp)    FTP    HTTP
    3. Structural variation (SV)    FTP    HTTP
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