FILE FORMATS
Supported File Types
Lasergene Molecular Biology and Lasergene Protein File Support:
Lasergene Genomics File Support:
GenVision Pro Imported and Exported File Types
SeqMan NGen Imported File Types
ArrayStar Imported File Types
ArrayStar Exported File Types
Below are the file formats supported for import and export by the applications within the Lasergene Molecular Biology and Lasergene Protein packages.
Imported File Types
| File Format | EditSeq | GeneQuest | GenVision | MegAlign | MegAlign Pro | PrimerSelect | Protean 3D | SeqBuilder Pro | SeqMan Pro | SeqNinja |
|---|---|---|---|---|---|---|---|---|---|---|
| 454 Life Sciences output files (*.sff; *.fas and *.qual) | ✓ | |||||||||
| ABI13 (*.abi, *.ab1, *.abd) | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||
| ALX (*.alx) | ✓ | |||||||||
| Clone Manager Suite (*.cm5) | ✓ | |||||||||
| DNA Multi-seq2 (*.mseq) | ✓7 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||
| EMBL8 (*.embl, *.txt) | ✓8 | ✓ | ||||||||
| Extended File of Files (*.eff) | ✓ | ✓8 | ||||||||
| FASTA Format (*.fasta, *.fas, *.fap, *.nt, *.aa) | ✓ | ✓11 | ✓ | ✓ | ✓ | ✓9 | ✓ | ✓11 | ✓ | |
| FASTA nucleic acid file 454/NCBI (*.fna) | ✓ | ✓8 | ✓ | |||||||
| FASTA Alignment with Gaps (*.fasta, *.fa, *.fas, *.fna, *.fap, *.nt, *.aa, *.frn, *.faa, *.ffn, *.mfa) | ✓ | |||||||||
| File of Filenames3 (*.fof) | ✓ | ✓ | ✓ | ✓ | ✓ | |||||
| GCG (*.seq, *.gcg, *.pro, *.pep) | ✓7 | ✓ | ✓8 | |||||||
| GCG Pileup (*.msf) | ✓ | |||||||||
| GenBank (*.gbk, *.gb, .gp, .gpwithparts, .gbwithparts, *.genbank, *.genpept) | ✓ | ✓11 | ✓8 | ✓ | ✓8 | ✓ | ✓ | ✓8 | ✓ | |
| Geneious (*.geneious) | ✓ | |||||||||
| GeneQuest Doc5(*.dad) | ✓8 | ✓ | ✓10 | ✓ | ✓10 | ✓ | ✓11 | |||
| GenVision Project Files (*.gnv) | ✓ | |||||||||
| Gzip1 (*.gz) | ✓ | ✓7 | ||||||||
| Lasergene DNA (*.seq) | ✓7 | ✓7 | ✓7 | ✓ | ✓7 | ✓7 | ✓ | ✓ | ||
| Lasergene Protein(*.pro) | ✓7 | ✓7 | ✓ | ✓ | ✓7 | ✓ | ✓ | |||
| MacVector Format (*.nucl, *.prot) | ✓ | |||||||||
| MapDraw Doc5(*.mpd) | ✓8 | ✓ | ✓10 | ✓ | ✓10 | ✓ | ✓11 | |||
| MegAlign Doc5(*.meg) | ✓8 | ✓ | ✓ | ✓ | ✓10 | ✓9 | ✓ | ✓11 | ||
| MegAlign Pro Format (*.msa) | ✓ | |||||||||
| mmCIF Format (*.cif) | ✓ | |||||||||
| NovaFold Format (*.novafold) | ✓ | |||||||||
| NovaFold Antibody Format (*.antibody) | ✓ | |||||||||
| NovaDock Format (*.novadock) | ✓ | |||||||||
| Phred (*.phd.) | ✓ | ✓10 | ✓10 | ✓8 | ✓ | |||||
| PrimerSelect Doc5(*.pcr) | ✓8 | ✓ | ✓10 | ✓ | ✓ | ✓9 | ✓ | ✓11 | ||
| Protean 3D Structure Files (*.structure) | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||
| Protean Docs (*.pad) | ✓12 | ✓10 | ✓ | ✓10 | ✓ | ✓ | ||||
| Protein Data Bank files (*.pdb, *.ent, *.pdb.gz, *.ent.gz, *.zip, *.txt) | ✓14 | |||||||||
| RNA Fold files (*.ct) | ✓ | |||||||||
| SCF24 (*.scf) | ✓ | |||||||||
| SCF3 (*.scf) | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||
| SeqBuilder Doc5(*.sbd) | ✓8 | ✓ | ✓10 | ✓ | ✓10 | ✓9 | ✓ | ✓11 | ||
| SeqBuilder Gel Files5 (*.sbgel) | ✓ | |||||||||
| SeqBuilder Project5(*.sbp) | ✓ | ✓ | ✓ | |||||||
| SeqMan Pro Docs (*.sqd) | ✓8 | ✓ | ||||||||
| SeqNinja Docs (*.star) | ✓ | ✓ | ||||||||
| SeqNinja Feature Table Files (*.starff) | ✓ | |||||||||
| Sequencher 4.2 Assembly Projects (*.spf) | ✓ | |||||||||
| SnapGene (*.dna, *.prot) | ✓ | |||||||||
| Text (*.txt)8 | ✓8 | ✓ | ✓ | ✓8 | ||||||
| VCF (*.vcf) | ✓ | |||||||||
| VectorNTI (*.gb, *.gp, *.ma4, *.pa4) | ✓ | |||||||||
| Zip1 (*.zip) | ✓8 | ✓ | ✓ | ✓ | ✓ | ✓7 | ✓ |
1 Only zip files containing ABI, SCF3, Lasergene protein or Lasergene DNA files. All other files will be ignored.
2 Multiple Lasergene DNA sequence files can be created by EditSeq, SeqMan Pro, and MegAlign.
3 FOF can not contain reference to another multiple sequence file format such as FastA, DNA* mseq, or Zip.
4 Program will translate to BAF.
5 Referred to collectively as “Lasergene Documents” in “Files of Type” or “Show pull-down menus”.
7 GenBank formatted features will be parsed.
8 Through “drag and drop” only. These files are not supported through the menu system.
9 Projects or files must contain protein sequence data.
10Only the sequence, features and comments of the file will be read in.
11Only DNA sequences will be read in.
12Only read in Macintosh.
13Lasergene does not support ABI files without base calls.
14Protean 3D supports version 3.2 of PDB files.
Exported File Types
| File Format | EditSeq | GeneQuest | GenVision | MegAlign | MegAlign Pro | PrimerSelect | Protean 3D | SeqBuilder Pro | SeqMan Pro | SeqNinja |
|---|---|---|---|---|---|---|---|---|---|---|
| Distance Matrix Files (*.csv, *.tab) | ✓ | |||||||||
| DNA Multi-seq (*.mseq) | ✓ | ✓ | ✓ | |||||||
| EMBL (*.embl, *.txt) | ✓ | |||||||||
| Extended File of Files (*.eff) | ✓ | |||||||||
| FASTA Format (*.fas, *.fap, *.fna, *.fasta) | ✓17 | ✓17 | ✓17 | ✓ | ✓17 | ✓17 | ✓ | |||
| FASTA Alignment with Gaps (*.fasta, *.fa, *.fas, *.fna, *.fap, *.nt, *.aa, *.frn, *.faa, *.ffn, *.mfa) | ✓ | |||||||||
| File of Filenames (*.fof) | ✓ | |||||||||
| GCG (*.gcg) | ✓ | ✓ | ||||||||
| GCG Pileup Files (*.msf) | ✓ | ✓ | ||||||||
| GCG Protein File (*.pep) | ✓ | |||||||||
| GenBank (*.gbk, *.gb, *.gp, *.genbank, *.genpept, *.gpwithparts, *.gbwithparts, *.gbf, *.gbff) | ✓19 | ✓19 | ✓ | ✓19 | ✓19 | ✓ | ||||
| GeneQuest Doc (*.dad, *.dao) | ✓ | ✓15 | ||||||||
| GenVision – Data Visualization (*.gnv) | ✓ | ✓ | ||||||||
| Image Files (*.png, *.jpg, *.gif) | ✓20 | ✓ | ||||||||
| Lasergene DNA (*.seq) | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||
| Lasergene Protein(*.pro) | ✓ | ✓ | ✓ | ✓ | ||||||
| MegAlign Doc (*.meg) | ✓15 | ✓ | ✓ | ✓15 | ||||||
| MegAlign Pro Format (*.msa) | ✓ | |||||||||
| mmCIF Format (*.cif) | ✓ | |||||||||
| Newick Tree File (*.newick) | ✓ | |||||||||
| Nexus Format (*.nex, *.nxs) | ✓ | |||||||||
| NovaFold Format (*.novafold) | ✓ | |||||||||
| PAUP 3.0 Files (*.pau) | ✓18 | |||||||||
| PAUP 4.0 Files (*.nex) | ✓ | |||||||||
| Phylip Distance Matrix Files (*.dist) | ✓ | |||||||||
| Phylip Tree Files (*.dnd) | ✓ | |||||||||
| Portable Document Format(*.pdf) | ✓ | ✓ | ✓ | |||||||
| PostScript Files (*.ps) | ✓ | |||||||||
| PowerPoint (*pptx) | ✓ | ✓ | ||||||||
| Primer Catalog (*.pri) | ✓ | |||||||||
| PrimerSelect Doc (*.pcr) | ✓15 | ✓ | ✓15 | |||||||
| Protean 3D Structure Files (*.structure) | ✓ | |||||||||
| Protean Docs (*.pad, *.pao) | ✓15 | |||||||||
| Protein Data Bank files (*.pdb) | ✓ | |||||||||
| RNA Fold files (*.ct) | ✓ | |||||||||
| SeqBuilder Doc (*.sbd) | ✓15 | ✓ | ||||||||
| SeqBuilder Project (*.sbp) | ✓ | |||||||||
| SeqBuilder Gel (*.sbgel) | ✓ | |||||||||
| SeqMan Pro Docs (*.sqd) | ✓ | |||||||||
| SeqNinja Docs (*.star) | ✓ | |||||||||
| SeqNinja Feature Table Files (*.starff) | ✓ | |||||||||
| Text (*.txt) | ✓ | |||||||||
| VCF (*.vcf) | ✓ | |||||||||
| Video Files (*.mov, *.avi) | ✓ |
15File-Save will save back as original file type
16 *.fap only
17 *.fas only
18 Only the alignment report.
19 *.gbk only
20 *.png and *.jpg only
GenVision Pro
Below are the file types supported for import and export by GenVision Pro, an application included within Lasergene Genomics.
Imported File Types
| File Format | File Extension(s) |
|---|---|
| BED files | *.bed |
| FASTA files | *.fasta |
| GenBank files | *.gbk |
| GenVision “box” files | *.txt |
| GenVision Pro files | *.gvp |
| SeqMan NGen assembly files | *.assembly |
| SeqNinja Feature Table Files1 | *.starff |
| Wiggle files | *.wig |
1 Files with the same name as an imported FASTA file and located in the same directory will be imported automatically.
Exported File Types
| File Format | File Extension(s) |
|---|---|
| GenVision Pro files | *.gvp |
| Image files | *.pdf, *.png, *.jpg. *.pptx (PowerPoint) |
SeqMan NGen
SeqMan NGen is included within Lasergene Genomics. Below are the file types supported for import for both normal workflows and special workflows.
Note: SeqMan NGen supports the export of data in .sqd, .bam, and .fas formats and can generate reports in .txt format.
Table 1: File Types Imported by SeqMan NGen for De Novo Assemblies and Templated Alignments (Special Workflows)
| File Format | File Extension(s) | Reads | Template Sequences | Layout File | Vectors, Repeats, and Contaminant Sequences |
|---|---|---|---|---|---|
| Illumina (scarf and fastq) | *_qseq.txt, *.txt | yes | no | no | yes |
| Roche 4542 | *.fas, *.fna | yes | yes | no | yes |
| Roche 454 Std. Flow Files2 | *.sff | yes | yes | no | no |
| SOLiD | *.gff, *.bam | yes | no | yes | no |
| Pacific Biosciences | *bas.h5, *bax.h5, *.fastq, *.fasta | yes | yes | no | no |
| Ion Torrent | *.bam, *.fastq | yes | yes | no | no |
| SeqMan Pro | *.sqd | yes | yes | no | no |
| Phred | *.phd | yes | yes | no | no |
| Lasergene | *.seq, *.sbd | yes | yes | no | yes |
| ABI1 | *.abi, *.ab1, *.abd | yes | yes | no | yes |
| FASTA2 | *.fas, *.nt, *.txt, *.fna, *.fasta | yes | yes | no | yes |
| FASTQ | *.fasq | yes | yes | no | yes |
| File of Filenames | *.fof | yes | yes | yes | yes |
| SCF2 and SCF3 | *.scf | yes | yes | no | yes |
| Text | *.txt | yes | yes | no | yes |
| GenBank | *.gbk, *.gb, *.gbff | no | yes | no | yes |
| GCG | *.seq, *.gcg | yes | yes | no | yes |
Table 2: File Types Imported by SeqMan NGen for Templated Alignments (Normal Workflows)
| File Format | File Extension(s) | Reads3 | Template Sequences | Layout File |
|---|---|---|---|---|
| Illumina (scarf and fastq) | *_qseq.txt, *.txt | yes | no | no |
| Ion Torrent | *.bam, *.fastq | yes | no | no |
| Pacific Biosciences | *bas.h5, *bax.h5, *.fastq, *.fasta | yes | no | no |
| Roche 4542 | *.fas, *.fna | yes | no | no |
| Roche 454 Std. Flow Files2 | *.sff | yes | no | no |
| SeqMan Pro | *.sqd | no | yes | no |
| FASTA2 | *.fas, *.nt, *.txt, *.fna, *.fasta | yes | yes | no |
| FASTQ | *.fasq | yes | no | no |
| GenBank | *.gbk, *.gb, *.gbff | no | yes | no |
| General Feature Format4 | *.gff, *.gff3 | yes | no | no |
| BAM | *.bam | no | no | yes |
1 SeqMan NGen does not support ABI files without base calls.
2 Should have an associated .qual file with the same file name and a .qual extension. The .qual file must be in the same folder with the sequence file in order for the quality scores to be used.
3 For “Reference-guided assembly with gap closure” assembly type, paired-end or mate-pair data is required. Reads must be 100bp minimum.
4 Requires a FASTA in the same directory.
ArrayStar
ArrayStar is included within Lasergene Genomics. Below are the file types supported for import and export by each application.
Imported File Types
| File Format | File Extension(s) | Variants | Microarray | QSeq (ChIP-Seq, CNV, miRNA, RNA-Seq) | Attributes | Annotations | VCF SNP |
|---|---|---|---|---|---|---|---|
| ABI SOLiD files | *.gff, *.csfasta | ✓1 | |||||
| Affymetrix Annotation files | *.csv, *.transcript.csv | ✓ | |||||
| Affymetrix Attributes files | *.arr | ✓ | |||||
| Affymetrix CHP files2 / Normalized Signal Values | *.chp | ✓ | ✓ | ✓ | |||
| Affymetrix MAGE-ML files3 | *.xml | ✓ | ✓ | ||||
| Affymetrix read files (unnormalized)4 | *.cel | ✓ | ✓ | ✓ | |||
| Agilent/Feature Extraction files5 | *txt | ✓ | ✓ | ✓ | |||
| Applied Biosystems (ABI) files6 | *.abi, *.ab1, *abd | ✓1 | |||||
| ArrayStar and QSeq projects | *.dmaproj,*.astar | ✓ | ✓ | ✓ | |||
| BED files | *.bed | ✓ | |||||
| ClustalW Alignment files | *.aln | ✓ | |||||
| dbNSFP Gene files | dbNSFP*_gene | ✓ | |||||
| DNA Multi-seq files7 | *.mseq | ✓ | |||||
| ELAND Alignment files | *.txt | ✓ | |||||
| EMBL files | *.embl, *txt | ✓8 | |||||
| FastA files | *.fas, *.fa,*.nt, *txt | ✓ | |||||
| FastQ files | *.fastq | ✓1 | |||||
| File of Filenames (FOF) | *.fof | ✓ | |||||
| GCG files | *.seq, *.gcg | ✓8 | |||||
| GenBank files | *.gbk, *.gb | ✓ | |||||
| Gene Ontology (GO) Annotation files | *.gene_association.*; *.goa | ✓ | |||||
| GenePix Results files9 | *.gpr | ✓1 | ✓1 | ✓1 | |||
| GeneQuest projects | *.dad | ✓8 | |||||
| General Feature Format files | *.gff | ✓ | |||||
| HapMap Genotype SNP Table Text files10 | *.txt | ✓ | ✓ | ||||
| Helicos files | *.fa, *.txt | ✓1 | |||||
| Illumina Alignment files | *.txt | ✓ | |||||
| Illumina Bead Studios files11 | N/A | ✓ | |||||
| Illumina Microarray files12 | *.csv, *.txt | ✓ | ✓ | ✓ | |||
| Illumina Sequence files | *.fastq, *.fas, *txt, *.qseq.txt | ✓1 | |||||
| Lasergene DNA files | *.seq | ✓8 | |||||
| Misc. comma-separated files13 | *.csv | ✓ | ✓ | ✓ | ✓ | ||
| Misc. text files14 | *.txt | ✓ | ✓ | ✓ | ✓ | ||
| Phred files | *.phd | ✓ | |||||
| Roche 454 files | *.fna, *.fas, *.sff | ✓1 | |||||
| Roche NimbleGen Design files | *.ngd | ✓ | ✓ | ||||
| Roche NimbleGen files15 | *.call, *.calls | ✓ | ✓ | ✓ | |||
| Roche NimbleGen text files16 | *.txt | ✓ | ✓ | ✓ | ✓ | ||
| Roche NimbleGen files (unnormalized)17 | *.pair, *.pair.txt | ✓ | ✓ | ✓ | |||
| SAM and BAM assembly files | *.sam, *.bam | ✓ | |||||
| SeqBuilder projects | *.sbd, *.sbp | ✓8 | |||||
| SeqMan NGen assembly files 18 | *.assembly | ✓ | ✓ | ✓ | ✓ | ||
| SeqMan Pro SNP Table text files19 | *.txt | ✓ | ✓ | ||||
| SeqMan Pro Variant Call Files (VCF) 20 | *.vcf | ✓ | ✓ | ||||
| Single Configuration (SCF2/SCF3) files | *.scf | ✓1 | |||||
| VCF Annotation files | *.vcf | ✓ | ✓ | ✓ | |||
| VectorNTI files | *.gb | ✓8 |
1 Reads only.
2 Supported CHP files for import include: Affymetrix GCOS files, Affymetrix GCCC (Calvin) files, “Quantification-only” CHP files that are the result of doing PLIER or RMA normalization on Affymetrix .cel files, “Whole-transcript” CHP files that contain information for whole-transcript arrays
3 To be readable in ArrayStar, the MAGE-ML *.dtd file must be present in the same folder as the Attributes file.
4 Contains un-normalized signal data from Affymetrix. In order to interpret and normalize data from .cel files, ArrayStar requires a .cdf file (for 3’ expression chip types) or a .pgf file (for whole-transcript arrays).
5 Contains data from one chip with one or two color channels.
6 ArrayStar does not support ABI files without base calls.
7 ArrayStar does not recognize features saved in *.mseq files as annotations.
8 Template only.
9 Contains data from one chip with two color channels. When importing *.gpr files, ArrayStar uses the linear values from the “Ratio of Medians” column as the signal intensity values.
10 Imported from HapMap via the Data Import Wizard.
11 See ArrayStar Help for more information.
12 Contains either gene-level data (“Group Gene Profile” or “Sample Gene Profile”) or probe-level data (“Group Probe Profile” or “Sample Probe Profile”).
13 Any user-defined, comma-delimited text files containing annotation or expression data.
14 Any user-defined text files containing annotation or expression data.
15 Contains expression data for single or multiple chips.
16 NimbleGen CALL-type files in TXT format. “NimbleGen Sample Key” is a type of Attributes file. For microarray projects, Attributes files may contain expression data for single or multiple chips.
17 An unnormalized file with probe level data.
18 Includes SNP data plus detailed feature, MID-tag, and sample name information.
19 Created by opening a SeqMan NGen *.assembly in SeqMan Pro and exporting SNP data. The resulting *.txt file contains SNP data, as well as basic MID-tag and feature information.
20 Created in SeqMan Pro, or obtained via free download from the 1100 Genomes Project and the NHLBI Exome Sequencing Project (ESP).
Exported File Types
| File Format | File Extension(s) | Variants | Microarray | QSeq (ChIP-Seq, CNV, miRNA, RNA-Seq) |
|---|---|---|---|---|
| Affymetrix CHP files / Normalized Signal Values | *.chp | ✓ | ✓ | ✓ |
| ArrayStar and QSeq projects | *.dmaproj,*.astar | ✓ | ✓ | ✓ |
| BED files1 | *.bed | ✓ | ||
| GenBank files | *.gbk, *.gb | ✓2 | ||
| General Feature Format files1 | *.gff | ✓ | ||
| GenVision projects3 | *.gnv, *.txt | ✓ | ||
| Misc. comma-separated files4 | *.csv | ✓ | ✓ | ✓ |
| Misc. text files4 | *.txt | ✓ | ✓ | ✓ |
| Roche NimbleGen files5 | *.txt | ✓ | ✓ | ✓ |
| Template and sequence files | *.fas | ✓ | ||
| Wiggle files3 | *.wig | ✓ |
1 Must be selected in Configure Advanced Options before processing.
2 Template only.
3 Export is in a graph format. Must be selected in Configure Advanced Options before processing.
4 Only available in Gene Table view.
5 NimbleGen CALL-type files in TXT format.