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24 2.2.2 CHAPTER 2. RETRIEVING AND STORING DATA Data input formats Geneious version 7.0 can import the following file formats: Format BED Common Assembly Format Clustal CSFASTA DNAStar DNA Strider Embl/UniProt Endnote (8.0) XML FASTA FASTQ GCG GenBank Geneious Geneious Education GFF MEGA Molecular structure Newick Nexus PDB PDF Phrap ACE PileUp PIR/NBRF Qual Raw sequence text Rich Sequence Format Comma/Tab Separated Values SAM/BAM Sequence Chromatograms VCF Vector NTI sequence Vector NTI/AlignX alignment Vector NTI Archive Vector NTI/ContigExpress Vector NTI database Extensions *.bed *.caf *.aln *.csfasta *.seq, *.pro *.str *.embl, *.swp *.xml *.fasta, *.fas, etc. *.fastq, *.fasq *.seq *.gb, *.xml *.xml, *.geneious *.tutorial.zip *.gff *.meg *.pdb, *.mol, *.xyz, *.cml, *.gpr, *.hin, *.nwo *.tre, *.tree, etc. *.nxs, *.nex *.pdb *.pdf *.ace *.msf *.pir *.qual *.seq *.rsf *.csv, *.tsv *.sam, *.bam *.ab1, *.scf *.VCF *.gb, *.gp *.apr *.ma4, *.pa4, *.oa4, *.ea4, *.ca6 *.cep VNTI Database Data types Annotations Contigs Alignments Color space FASTA Nucleotide & protein sequences Sequences Sequences Journal article references Sequences, alignments Sequences with quality Sequences Nucleotide & protein sequences Preferences, databases Tutorial, assignment etc. Annotations Alignments Common sources UCSC Sequencher ClustalX ABI SOLiD DNAStar DNA Strider (Mac program), ApE Embl, UniProt Endnote, Journal article websites PAUP*, ClustalX, BLAST, FASTA Solexa/Illumina GCG GenBank Geneious Geneious Sanger Artemis MEGA 3D molecular structures Phylogenetic trees Trees, Alignments 3D Protein structures Documents, presentations Contig assemblies Alignments Sequences, alignments Quality file Sequences Sequences, alignments Spreadsheet files Contigs Raw sequencing trace & sequence Annotations Nucleotide & protein sequences Alignments Nucleotide & protein sequences, enzyme sets and publications Nucleotide sequence assemblies Nucleotide & protein sequences, enzyme sets and publications 3D structure databases and programs PHYLIP, Tree-Puzzle, PAUP*, ClustalX PAUP*, Mesquite, MrBayes & MacClade SP3, SP2, SPARKS, Protein Data Bank Adobe Writer, LATEX, Miktex Phrap/Consed pileup (gcg) NBRF PIR Associated with a FASTA file Any file that contains only a sequence GCGs NetFetch Microsoft Excel SAMtools Sequencing machines 1000 Genomes Project Vector NTI Vector NTI, AlignX Vector NTI Vector NTI Vector NTI BED format The BED format contains sequence annotation information. You can use a BED file to annotate existing sequences in your local database, import entirely new sequences, or import the annotations onto blank sequences. CLUSTAL format The Clustal format is used by ClustalW [24] and ClustalX [23], two well known multiple sequence alignment programs. Clustal format files are used to store multiple sequence alignments and contain the word clustal at the beginning. An example Clustal file: CLUSTAL W (1.74) multiple sequence alignment
