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Public Reference Databases

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Contents

Available References and Tracks in GenomeQuest

  • The following genomes and tracks are available through the regular hotdrive processes, and accessible through specific workflows in the GenomeQuest web interface:


  • Bacillus licheniformis ATCC 14580:
    • Blichen Proteins and Genes Tracks


  • Bacillus subtilis subsp. subtilis str. 168:
    • Bsubtilis Proteins and Genes Track


  • Escherichia coli BL21-Gold(DE3)pLysS AG chromosome:
    • EcoliBL21 Proteins and Genes Track


  • Escherichia coli K-12 MG1655 chromosome NC_000913.2:
    • Escherichia coli K-12 MG1655 Genes Track


  • Arabidopsis thaliana araTha1:
    • Arath CDS, Exons, Genes, Splice Sites tracks


  • Bos taurus Baylor build 4 bosTau4:
    • Cow CDS, Exons, Genes, Splice Sites tracks


  • Canis lupus familiaris Broad build canFam2:
    • Dog CDS, Exons, Genes, Splice Sites tracks


  • Gallus gallus WGUSC build 2.1 galGal3:
    • Chicken CDS, Exons, Genes, Splice Sites tracks


  • Homo sapiens NCBI36.3 (hg18):
    • Human CDS, Exons, Genes, Splice Sites tracks (hg18)
    • dbSNP130 (hg18)
    • Human Cosmic Somatic Mutations (hg18)
    • Human OMIM genes (hg18)
    • Human Repeats (hg18)
    • Genetests NGS diagnostic panel (hg18)


  • Homo sapiens GRCh37.2 (hg19):
    • Genetests NGS diagnostic panel (hg19)
    • Human CDS, Exons, Genes, Splice Sites tracks (hg19)
    • dbSNP131 (hg19)
    • Human OMIM genes (hg19)
    • Human Repeats (hg19)
    • Human Cosmic Somatic Mutations (hg19)
    • SIFT pathogenicity prediction (hg19)
    • 1000 Genomes (hg19)
    • POLYPHEN pathogenicity prediction (hg19)


  • Mus musculus NCBI build 37 (mm9):
    • Mouse CDS, Exons, Genes, Splice Sites tracks
    • Mouse dbSNP128 track
    • Mouse repeat track


  • Rattus norvegicus Baylor build 3.4 (rn4):
    • No tracks available


IP and Sequence Search Subject Databases:

  • The following databases are available through the sequence searching workflows. Not all content is available to each:


  • RefSeq Genomic- It is generally unnecessary to search genomes for IP searches, especially large plant and mammalian genomes.
  • GQGene- It is composed of transcripts (already available in GenBank) and parts of genomes.
  • DrugBank- A database of drugs and their targets. DrugBank is auto-searched for IP searches. GenomeQuest utilizes an advanced and unreleased version of DrugBank called DrugBank Pro to get you the sharpest accuracy. Please read more about DrugBank Pro here.


Selectable Databases:

  • When you choose Patent databases only patent databases are selected. When you select Patents and Public Reference databases, the following databases are selected because we believe that those reference databases represent the best set of non-genomic databanks with minimized redundancy:


  • GQPAT- (GQ Pat Premium or GQ Pat)
  • Protein Data Bank


  • GenBank Core Divisions (Nucleotide):
    • GenBank Main Divisions (nt)
    • Genbank - Bacterial division
    • Genbank - Environmental Samples
    • Genbank - High-throughput cDNA division
    • Genbank - Invertebrate division
    • Genbank - Other Mammalian division
    • Genbank - Bacteriophage division
    • Genbank - Plant division (plant fungal algal)
    • Genbank - Primate division
    • Genbank - Rodent division
    • GB SET
    • Genbank - Synthetic division
    • Genbank - Unannotated division
    • Genbank - Viral division
    • Genbank - Other Vertebrate division
    • GenBank Others
    • Genbank - Expressed Sequence Tags division
    • Genbank - High-throughput Genomic sequences division
    • Genbank - Genome Survey Sequences division
    • Genbank - Sequence Tagged Sites division


  • Protein Databases:
    • Reference Databases
    • Uniprot
    • Swiss-Prot - from Expasy
    • Translated EMBL - from Expasy
    • Swiss-Prot varsplic - from Expasy
    • RefSeq - Protein
    • Genpept - Translated Genbank
    • DrugBank Pro protein sequences
    • Protein Data Bank - protein seqs


  • GQ Gene:
    • Human - Homo_sapiens
      • GQ Gene for Homo_sapiens
      • GQ Gene Transcripts for Homo sapiens
    • Mouse - Mus_musculus
      • GQ Gene for Mus_musculus
      • GQ Gene Transcripts for Mus musculus
    • Rat - Rattus_norvegicus
      • GQ Gene for Rattus_norvegicus
      • GQ Gene Transcripts for Rattus norvegicus
    • Dog - Canis_familiaris
      • GQ Gene for Canis_familiaris
      • GQ Gene Transcripts for Canis familiaris
    • Rice - Oryza_sativa
      • GQ Gene for Oryza_sativa
      • GQ Gene Transcripts for Oryza sativa
    • Arabidopsis - Arabidopsis_thaliana
      • GQ Gene for Arabidopsis_thaliana
      • GQ Gene Transcripts for Arabidopsis thaliana
    • Corn - Zea_mays
      • GQ Gene for Zea_mays
      • GQ Gene Transcripts for Zea mays
      • Zea mays genomic
    • Sorghum - Sorghum_bicolor
      • GQ Gene for Sorghum_bicolor
      • GQ Gene Transcripts for Sorghum_bicolor
      • Sorghum bicolor genomic
    • Soybean - Glycine_max
      • GQ Gene for Glycine_max
      • GQ Gene Transcripts for Glycine_max
      • Glycine max genomic


  • Genomes Vertebrate:
    • Bos taurus Baylor build 4 bosTau4
    • Canis lupus familiaris Broad build canFam2
    • Danio rerio Zv8 danRer6
    • Gallus gallus WGUSC build 2.1 galGal3
    • Homo sapiens GRCh37.2 (hg19)
    • Homo sapiens NCBI36.3 (hg18)
    • Mus musculus NCBI build 37 (mm9)
    • Pan troglodytes CGSC build 2.1 panTro2
    • Rattus norvegicus Baylor build 3.4 (rn4)


  • Genomes Microbial:
    • Bacillus licheniformis ATCC 14580 complete genome
    • Bacillus subtilis subsp. subtilis str. 168 complete genome
    • Escherichia coli BL21-Gold(DE3)pLysS AG chromosome complete genome


  • Genomes Plant:
    • Arabidopsis thaliana araTha1
    • Glycine max glyMax1
    • Oryza sativa Japonica cultivar: Nipponbare
    • Sorghum bicolor sorBic1
    • Zea mays release-4a.53
    • Zea mays RefGen_v2


Adding Content:

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