Imported File Types

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.
10 Only the sequence, features and comments of the file will be read in.
11 Only DNA sequences will be read in.
12 Only read in Macintosh.
13 Lasergene does not support ABI files without base calls.
14 Protean 3D supports version 3.2 of PDB files.
15 Available for sequences to support gap closure.

Exported File Types

1 File-Save will save back as original file type.
2 *.fas only.
3 Only the alignment report.
4 *.gbk only.
5 *.png and *.jpg only.
6 Available for consensus sequences.
7 Available for tables.

GenVision Pro

Below are the file types supported for import and export by GenVision Pro, an application included within Lasergene Genomics.

Imported File Types

1 Files with the same name as an imported FASTA file and located in the same directory will be imported automatically.

Table 1: File Types Imported by SeqMan NGen for De Novo Assemblies and Templated Alignments (Special Workflows)

Table 2: File Types Imported by SeqMan NGen for Templated Alignments (Normal Workflows)

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.

Imported File Types

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

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.