Organize, search and share sequence databases
Arrange and browse your data library how you like.
- Add and remove sequence databases
- Document history automatically saved
- Batch export
- Batch rename
- Filter documents based on fields
- Share annotated sequence files
- Export and submit to Genbank
Import metadata onto sequences and other documents
Seamlessly attach new data from downstream analyses or other applications onto your sequences or update document fields, by importing columns from a CSV/TSV format spreadsheet onto documents that are already in Geneious Prime.
Smart NGS File Importing
Drop any assortment of SAM, BAM, GFF, BED, and VCF files into Geneious to import in one easy step, even if you have a mixture of different samples and reference sequences.
Wide ranging file format compatibility from FASTA to VectorNTI
Have data from multiple sources, including different sequencing machines and other sequence analysis software? Loading into Geneious Prime is easy with a simple drag and drop import of a vast range of formats.
Dedicated importer for Vector NTI Express and Advance databases preserves metadata, full database structure including subsets, and lineage information.
Supported Format Types
|Format||Extensions||Data Types||Common Sources|
|Common Assembly Format||*.caf||Contigs||Sequencher|
|Clone Manager||*.cm5||Nucleotide sequences||Clone Manager|
|CS FASTA||*.csfasta||Color space||FASTA ABI SOLiD|
|DNAStar||*.seq, *.pro||Nucleotide & protein sequences||DNAStar|
|DNA Strider||*.str||Sequences||DNA Strider|
|Embl/UniProt||*.embl, *.swp||Sequences||Embl, UniProt|
|Endnote (8.0) XML||*.xml||Journal article references||Endnote, Journal article websites|
|FASTA||*.fasta, *.fas, etc.||Sequences, alignments||PAUP*, ClustalX, BLAST, FASTA|
|FASTQ||*.fastq, *.fasq||Sequences with quality||Solexa/Illumina|
|GenBank||*.gb, *.xml||Nucleotide & protein sequences||GenBank|
|Geneious||*.xml, *.geneious||Preferences, databases||Geneious|
|Molecular structure||*.pdb, *.mol, *.xyz, *.cml, *.gpr, *.hin, *.nwo||3D molecular structures||3D structure databases and programs|
|Newick||*.tre, *.tree, etc.||Phylogenetic trees||PHYLIP, Tree-Puzzle, PAUP*, ClustalX|
|Nexus||*.nxs, *.nex||Trees, Alignments||PAUP*, Mesquite, MrBayes & MacClade|
|PDB||*.pdb||3D Protein structures||SP3, SP2, SPARKS, Protein Data Bank|
|Documents, presentations||Adobe Writer, LATEX, Miktex|
|Phrap ACE||*.ace||Contig assemblies||Phrap/Consed|
|PIR/NBRF||*.pir||Sequences, alignments||NBRF PIR|
|Qual||*.qual||Quality ﬁle||Associated with a FASTA ﬁle|
|Raw sequence text||*.seq||Sequences||Any ﬁle that contains only a sequence,|
|Rich Sequence Format||*.rsf||Sequences, alignments||GCGs NetFetch|
|Comma/Tab Separated Values||*.csv, *.tsv||Spreadsheet ﬁles||Microsoft Excel|
|Sequence Chromatograms||*.ab1, *.scf||Raw sequencing trace & sequence||Sequencing machines|
|SnapGene||*.dna||Sequences, annotations, metadata||SnapGene|
|Variant Call Format||*.vcf||Variant calls/SNPs||Variant callers and databases|
|Vector NTI sequence||*.gb, *.gp||Nucleotide & protein sequences||Vector NTI|
|Vector NTI/AlignX alignment||*.apr||Alignments||Vector NTI, AlignX|
|Vector NTI Archive||*.ma4, *.pa4, *.oa4, *.ea4, *.ca6||Nucleotide & protein sequences, enzyme sets and publications||Vector NTI|
|Vector NTI/ContigExpress||*.cep||Nucleotide sequence assemblies||Vector NTI|
|Vector NTI database||VNTI Database||Nucleotide & protein sequences, enzyme sets and publications||Vector NTI|
Export Format Options
Any set of documents may be exported in Geneious native format.
|DNA sequence||FASTA, Genbank XML, Genbank ﬂat, Geneious|
|Amino acid sequence||FASTA, Genbank XML, Genbank ﬂat, Geneious|
|Chromatogram sequence||ABI, Geneious|
|Sequence with quality||FastQ, Qual, Geneious|
|Annotation||GFF, BED, VCF, Geneious|
|Multiple sequence alignment||Phylip, FASTA, NEXUS, MEGA3, Geneious|
|Assembly||Phrap ACE, Geneious, SAM/BAM, Geneious|
|Phylogenetic tree||Phylip, FASTA, NEXUS, Newick, MEGA3, Geneious|
|PDF document||PDF, Geneious|
|Publication||EndNote 8.0, Geneious|
|Graphs||CSV or WIG, or images|
More Geneious Prime Features
BLAST / NCBI – Connect to NCBI and PubMed, submit sequences directly to GenBank, BLAST sequences and search your own database.
NGS Visualization and Analysis – Comprehensive analysis of data, including genome browser, contig visualization, SNP calling, and RNA-Seq expression analysis.
Alignment – Perform pairwise and multiple alignments of DNA or protein using trusted algorithms, including MAFFT and ClustalW.
Analysis and Annotation – Trim, assemble, annotate and view Sanger sequencing trace files
Molecular Cloning – View plasmid maps, automatically annotate vectors, find restriction sites; digest, ligate, and perform Golden Gate, Gibson, and Gateway cloning.
I really like your program. I first got it to make alignment and trees of my sequences and it works well for those purposes. But it was a real lifesaver a few weeks ago when I lost my academic license to Vector NTI and couldn’t access any of my plasmids!! But I noticed I could import my database into Geneious and I was back in business.
Coming from the world of Vector NTI, I must tell you that Geneious looks and feel much better!
It is so easy to search and then import GenBank files along with their annotations. The ability to stack information from various sources onto the same display for comparison purposes is invaluable. This may be in the form of multiple alignments or a a GenBank BLAST file with annotations superimposed on top of a protein sequence with all of the predicted protein properties displayed.