Geneious Prime is able to BLAST to many different databases held at NCBI. These databases are listed in the Tables 15.1 and 15.2 , and can be selected in the Databases drop down menu in the BLAST set up dialog. You must be able to connect to the internet from within Geneious Prime to BLAST to NCBI, and if you are behind a proxy server you may need to enter your proxy server settings under Tools → Preferences → Connection Settings, as described in Section 1.2.5 .
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| Database |
Nucleotide searches |
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| Nucleotide collection (nr) |
All non-redundant GenBank+EMBL+DDBJ+PDB sequences (no EST, STS, GSS or HTGS sequences) |
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| 16S ribosomal RNA |
16S rRNA sequences from bacteria and archaea |
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| 18S ribosomal RNA |
18S rRNA sequences (Fungal) |
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| 28S ribosomal RNA |
28S rRNA sequences (Fungal) |
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| Environmental samples (env_nt) |
Nucleotide sequences from large environmental sequence projects |
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| Expressed sequence tags (est) |
Database of GenBank + EMBL + DDBJ sequences from EST Divisions |
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| EST human |
Human subset of est |
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| EST mouse |
Mouse subset of est |
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| EST others |
Non-Human, non-mouse subset of est |
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| Genomic Survey Sequences (gss) |
Genome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences |
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| High Throughput Genomic Sequences (htgs) |
Unfinished HTGS: phases 0, 1 and 2 (finished, phase 3 HTG sequences are in nr) |
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| Human ALU repeat elements (alu_repeats) |
A small database of Human ALU repeat elements |
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| Human RefSeqGene (RefSeq_Gene) |
NCBI transcript reference sequences from human |
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| Internal transcribed spacer region (ITS) |
ITS region from fungal type and reference material |
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| NCBI Genomes (chromosome) |
Complete genomes and chromosomes from the NCBI Reference Sequence project. |
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| NCBI Reference Genomic Sequences (refseq_genomic) |
Genomic Reference sequences |
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| Patented Protein Sequences (pat) |
Nucleotide sequences derived from the Patent division of GenBank |
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| Protein Data Bank (PDB) |
Sequences derived from the 3D-structures of proteins from PDB |
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| Reference RNA (refseq_rna) |
NCBI Transcript Reference Sequences |
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| RefSeq Representative genomes |
Best quality and minimum redundancy genomes from NCBI Refseq Genomes |
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| Sequence Tagged Sites (dbsts) |
Database of GenBank+EMBL+DDBJ sequences from STS Divisions |
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| WGS Human |
Whole-genome shotgun contigs for Homo sapiens |
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| Database | Protein searches |
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| Nucleotide collection (nr) | All non-redundant GenBank coding region (CDS) translations+PDB+SwissProt+PIR+PRF |
| Metagenomic proteins (env_nr) | Translations of sequences in env_nt |
| Patented Protein Sequences (pat) | Protein sequences derived from the Patent division of GenBank |
| Protein Data Bank (PDB) | Sequences derived from 3D structure Brookhaven PDB |
| Reference Proteins (refseq_protein) | NCBI protein reference sequences |
| UniProtKB/SwissProt | Non-redundant protein sequences information from EMBL |
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