Gene Studio is a software for design and analysis of DNA molecules. It also allow to estimate molecular weight of a protein. It can be used for modeling of molecular cloning, sequence analysis and review of DNA molecules. Gene Studio can opens molecule files in FASTA and GeneBank format and stores information in XML files in GML format (Gene Studio Meta Language). The import from GeneBank format is complicated and sometimes not all genes can be marked by Gene Studio. It is NOT necessary and even NOT recommended to edit GML files manually, but here is the description of GML file format. The structure of GML file is shown on the listing 1.
<?xml version="1.0" ?> <GML version="1"> <MOLECULE NAME="Molecule name" SHOWORF="false" SHOWFEATURES="false" GROUPBY="10" SHOWRESTRICTION="true" LINEAR="true" DESCRIPTION=""> <FEATURE TYPE="2" ID="1" COLOR="ff00ff" NAME="feature1" FROM="1" TO="2" DIRECTION="true"/> <SEQUENCE>ATGC</SEQUENCE> </MOLECULE> </GML>
The root element is called "GML". It has only one attribute version which is always 1 for current Gene Studio version. The "MOLECULE" element contains all information about molecule. The attributes of this element ant it's description are shown in the table 1.
Attribute | Description |
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NAME | The name of this molecule for example pBR322; pSIM2, SUP35 etc. |
SHOWORF | Defines whether Gene Studio should show open reading frames. If both SHOWORF and SHOWFEATURES are true, open reading frames will be shown. |
SHOWFEATURES | Defines whether Gene Studio should show features. If true features will be shown. |
GROUPBY | Designates how nucleotide sequence will be grouped. In current version it can be grouped by 3 or by 10 nucleotides. |
SHOWRESTRICTION | Defines whether Gene Studio will show restriction sites. If true restriction sites will be shown even if SHOWFEATURES is false. |
LINEAR | If true molecule will be shown as linear, if false, molecular will be shown as a plasmid. |
DESCRIPTION | Is not used in current version of Gene Studio, but in future can be used to store information about molecule. |
"MOLECULE" element can have a set of elements called "FEATURE". These elements corresponds to some special regions marked on the DNA sequence by. For example it can be genes, promoters, ORFs, IRESs, etc. Gene Studio supports three types of features: gene, ORF and custom. Gene is drown as a bold arrow, ORF as a thin arrow and custom feature looks like box. Both gene and ORF will be shown as custom if there length on the map will be shorter then the length of gene and ORF arrowhead respectively. To describe feature element attributes from Table 2 are used.
Table2. The attributes of "FEATURE" element.Attribute | Description |
---|---|
ID | Unique identification number of a feature. |
TYPE | Can be 0, 1 and 2. 0 corresponds to Custom, 1 corresponds Gene and 2 corresponds ORF. |
COLOR | Defines the color of feature in three byte RGB format. Number should be in hexadecimal format. |
NAME | The name of a feature. |
FROM | The position of feature begin. It does not matter on which strand feature is located. FROM must be bigger then TO. |
TO | The position of feature end. Both FROM and TO must be bigger then 0 and not larger then sequence length. |
DIRECTION | True if feature located on the direct strand and false otherwise. |
The last child of "MOLECULE" element is "SEQUENCE". It contains the sequence of the molecule.