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 .

Table 15.1: Nucleotide BLAST databases


Nucleotide searches

Nucleotide collection (nr)

All non-redundant GenBank+EMBL+DDBJ+PDB sequences (no EST, STS, GSS or HTGS sequences)

16S ribosomal RNA

16S rRNA sequences from bacteria and archaea

18S ribosomal RNA

18S rRNA sequences (Fungal)

28S ribosomal RNA

28S rRNA sequences (Fungal)

Environmental samples (env_nt)

Nucleotide sequences from large environmental sequence projects

Expressed sequence tags (est)

Database of GenBank + EMBL + DDBJ sequences from EST Divisions

EST human

Human subset of est

EST mouse

Mouse subset of est

EST others

Non-Human, non-mouse subset of est

Genomic Survey Sequences (gss)

Genome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences

High Throughput Genomic Sequences (htgs)

Unfinished HTGS: phases 0, 1 and 2 (finished, phase 3 HTG sequences are in nr)

Human ALU repeat elements (alu_repeats)

A small database of Human ALU repeat elements

Human RefSeqGene (RefSeq_Gene)

NCBI transcript reference sequences from human

Internal transcribed spacer region (ITS)

ITS region from fungal type and reference material

NCBI Genomes (chromosome)

Complete genomes and chromosomes from the NCBI Reference Sequence project.

NCBI Reference Genomic Sequences (refseq_genomic)

Genomic Reference sequences

Patented Protein Sequences (pat)

Nucleotide sequences derived from the Patent division of GenBank

Protein Data Bank (PDB)

Sequences derived from the 3D-structures of proteins from PDB

Reference RNA (refseq_rna)

NCBI Transcript Reference Sequences

RefSeq Representative genomes

Best quality and minimum redundancy genomes from NCBI Refseq Genomes

Sequence Tagged Sites (dbsts)

Database of GenBank+EMBL+DDBJ sequences from STS Divisions

WGS Human

Whole-genome shotgun contigs for Homo sapiens

Table 15.2: Protein BLAST databases

Database Protein searches

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

   15.3.1 Edit BLAST Databases